diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/cloudbuild/build.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/cloudbuild/build.sh deleted file mode 100644 index 36ff64b0cf1e0d9499ff9de774522da1bdd5c8f3..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/cloudbuild/build.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/bash - -function is_expected_architecture() { - if [ $(uname -m) != "$1" ]; then - echo -e "\033[1;31;1mThe current script only supports execution on $1 architecture.\033[0m" - return 1 - fi -} - -function set_script_dir() { - local REL_SCRIPT_DIR - REL_SCRIPT_DIR="$(dirname "${BASH_SOURCE[0]}")" || return 1 - SCRIPT_DIR="$(cd "${REL_SCRIPT_DIR}" && pwd)" || return 1 -} - -function conda_initialize() { - __conda_setup="$("$1/bin/conda" 'shell.bash' 'hook' 2>/dev/null)" - if [ $? -eq 0 ]; then - eval "$__conda_setup" - else - if [ -f "$1/etc/profile.d/conda.sh" ]; then - . "$1/etc/profile.d/conda.sh" - else - export PATH="$1/bin:$PATH" - fi - fi - unset __conda_setup -} - -function main() { - is_expected_architecture aarch64 || return 1 - set_script_dir || return 1 - conda_initialize "$1" - conda build "$(dirname "$SCRIPT_DIR")/recipe" -} - -# /bin/bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/cloudbuild/build.sh /root/anaconda3 -main "$@" diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/conda-bld/kallisto-0.48.0-h0d531b0_1_kp.tar.bz2 b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/conda-bld/kallisto-0.48.0-h0d531b0_1_kp.tar.bz2 deleted file mode 100644 index 7a9bdfb1e572259daf13d941bdd3169b67e72546..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/conda-bld/kallisto-0.48.0-h0d531b0_1_kp.tar.bz2 and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/dependencies/DependencyList b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/dependencies/DependencyList deleted file mode 100644 index f3cd874d4aceb5b6d0c592be3dd0df770f4addeb..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/dependencies/DependencyList +++ /dev/null @@ -1 +0,0 @@ -DependencyPath Migrated diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\213\345\237\272\344\272\216conda\347\232\204kallisto\350\275\257\344\273\266\345\214\205\346\265\213\350\257\225\346\212\245\345\221\212.md" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\213\345\237\272\344\272\216conda\347\232\204kallisto\350\275\257\344\273\266\345\214\205\346\265\213\350\257\225\346\212\245\345\221\212.md" deleted file mode 100644 index 388267c9ec0db8c1af6788d557e9ff6eee3c02f0..0000000000000000000000000000000000000000 --- "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\213\345\237\272\344\272\216conda\347\232\204kallisto\350\275\257\344\273\266\345\214\205\346\265\213\350\257\225\346\212\245\345\221\212.md" +++ /dev/null @@ -1,67 +0,0 @@ -# Linux环境下基于conda的kallisto软件包测试报告 - -> 测试的主要思路是使用 x86 平台上命令执行的结果作为基准比对数据,与迁移成功后的鲲鹏平台上执行的结果进行比对。 - -[TOC] - -### 一、准备测试物料 - -1. **生成 x86 平台执行结果** - - *[生成完成请将结果移至鲲鹏平台进行下一步比对测试,其中测试用例数据来源于 [kallisto GitHub](https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz) ]* - - ![image-20220610165910443](images/image-report-001.png) - ![image-20220610170055797](images/image-report-002.png) - ![image-20220610170134255](images/image-report-003.png) - ![image-20220610170200202](images/image-report-004.png) - - ```shell - # 脚本的参数为当前系统的 Anaconda 或 Miniconda 的根路径 - # 脚本执行完成后会在 ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/TestCase 下载测试用例数据 - # 脚本执行完成后会在 ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/Expected 生成执行结果 - bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh /root/anaconda3 - ``` - -2. **生成 鲲鹏 平台执行结果** - - ![image-20220610170916459](images/image-report-005.png) - ![image-20220610171126315](images/image-report-006.png) - ![image-20220610171156048](images/image-report-007.png) - ![image-20220610171257281](images/image-report-008.png) - ![image-20220610171335183](images/image-report-009.png) - - ```shell - # 脚本的参数为当前系统的 Anaconda 或 Miniconda 的根路径 - # 脚本执行完成后会在 ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/Practical 生成执行结果 - bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh /root/anaconda3 - ``` - - -### 二、执行比对测试 - -![image-20220610171605541](images/image-report-010.png) -![image-20220610171820568](images/image-report-011.png) -![image-20220610171919491](images/image-report-012.png) -![image-20220610172001988](images/image-report-013.png) - -```shell -# 脚本的参数为当前系统的 Anaconda 或 Miniconda 的根路径 -# 主要实现鲲鹏平台下迁移成功的软件包执行结果与 x86 平台的执行结果的基准数据的比较 -bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/run_test.sh /root/anaconda3 -``` - -相关资源连接: - -conda 相关文档: https://docs.conda.io/en/latest/ - -conda: https://docs.conda.io/projects/conda/en/latest/ - -conda-build: https://docs.conda.io/projects/conda-build/en/latest/ - -ANACONDA.ORG: https://anaconda.org/ - -kallisto: https://pachterlab.github.io/kallisto/ - -pachterlab/kallisto GitHub: https://github.com/pachterlab/kallisto - -kallisto anaconda package: https://anaconda.org/bioconda/kallisto diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\213\345\237\272\344\272\216conda\347\232\204kallisto\350\275\257\344\273\266\345\214\205\350\277\201\347\247\273\346\214\207\345\215\227.md" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\213\345\237\272\344\272\216conda\347\232\204kallisto\350\275\257\344\273\266\345\214\205\350\277\201\347\247\273\346\214\207\345\215\227.md" deleted file mode 100644 index d78323c902f218ac7a3c7f6bf5100cd5eb677a47..0000000000000000000000000000000000000000 --- "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\213\345\237\272\344\272\216conda\347\232\204kallisto\350\275\257\344\273\266\345\214\205\350\277\201\347\247\273\346\214\207\345\215\227.md" +++ /dev/null @@ -1,456 +0,0 @@ -# Linux环境下基于conda的kallisto软件包迁移指南 - -> 本文档主要以 **bioconda/kallisto** 作为本次迁移演示用例,迁移的主要思路是基于 [**linux-64/kallisto-0.48.0-h0d531b0_1.tar.bz2**](https://anaconda.org/bioconda/kallisto/0.48.0/download/linux-64/kallisto-0.48.0-h0d531b0_1.tar.bz2) 的 **x86** 平台软件包,修改 **kallisto-0.48.0-h0d531b0_1/info/recipe/** 路径下的各配置文件,最后使用 [**Conda-build**](https://docs.conda.io/projects/conda-build/en/latest/) 进行软件包构建。在进行迁移构建之前请参考 [**《Linux环境中安装Anaconda.md》**](./Linux环境中安装Anaconda/Linux环境中安装Anaconda.md) 完成迁移环境搭建。 - -[TOC] - -### 一、准备迁移物料 - -1. **下载 kallisto x86 架构的软件包** - - *[请在 [**ANACONDA.ORG**](https://anaconda.org/) 搜索所需要的软件包]* - - ![image-guide-001.png](images/image-guide-001.png) - - *[下载最新版本的支持 linux-64 的软件包,且 Uploader 时间距离当前时间较近的软件包 ]* - - ![image-guide-002.png](images/image-guide-002.png) - - - **使用 curl 下载** - - ![image-guide-003.png](images/image-guide-003.png) - - ```shell - curl -L -o /home/KunpengCompute/Download/kallisto-0.48.0-h0d531b0_1.tar.bz2 https://anaconda.org/bioconda/kallisto/0.48.0/download/linux-64/kallisto-0.48.0-h0d531b0_1.tar.bz2 - ``` - - - **使用 wget 下载** - - ![image-guide-004.png](images/image-guide-004.png) - - ```shell - wget -O /home/KunpengCompute/Download/kallisto-0.48.0-h0d531b0_1.tar.bz2 https://anaconda.org/bioconda/kallisto/0.48.0/download/linux-64/kallisto-0.48.0-h0d531b0_1.tar.bz2 - ``` - - - **使用 HTTPie下载** *[请确保您已安装HTTPie]* - - ![image-guide-005.png](images/image-guide-005.png) - - ```shell - # 在 openEuler release 20.03 (LTS-SP3) 上安装 HTTPie - # 请确保您拥有 Python 3.7 或更新版本 ( python --version) - python3 -m pip install --upgrade pip - python3 -m pip install wheel - python3 -m pip install httpie - - # 下载 kallisto-0.48.0-h0d531b0_1.tar.bz2 - http --default-scheme=https --follow --all --print b --download --continue --output /home/KunpengCompute/Download/kallisto-0.48.0-h0d531b0_1.tar.bz2 https://anaconda.org/bioconda/kallisto/0.48.0/download/linux-64/kallisto-0.48.0-h0d531b0_1.tar.bz2 - ``` - -2. **clone hpc 项目并创建kallisto 迁移项目工程目录结构** - - ```shell - # git clone hpc 项目到 /home/KunpengCompute - # [在实验机环境下需要禁用 git 的 SSL校验,可使用以下命令禁用:git config --global http.sslVerify false] - git clone https://gitee.com/openeuler/hpc.git /home/KunpengCompute - # 创建 kallisto 迁移项目工程目录结构,如下 - # 有关目录结构的创建请参考相关 SOW 任务书中的描述 - ## /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1 - ## ├── cloudbuild/ - ## ├── conda-bld/ - ## ├── dependencies/ - ## │   └── DependencyList - ## ├── documentation/ - ## │   ├── images/ - ## │   ├── Linux环境下基于conda的kallisto软件包测试报告.md - ## │   ├── Linux环境下基于conda的kallisto软件包迁移指南.md - ## │   └── Linux环境中安装Anaconda/ - ## └── test/ - ``` - -3. **解压软件包** *[确保已安装以下软件包 sudo dnf install -y tar bzip2]* - - ![image-guide-006.png](images/image-guide-006.png) - - ```shell - # 解压压缩包中的 recipe 目录到 /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1 - tar -C /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1 -xjf /home/KunpengCompute/Download/kallisto-0.48.0-h0d531b0_1.tar.bz2 info/recipe/ --strip-components 1 --no-same-owner - ``` - -### 二、修改配置文件 - -1. **根据 X86 软件包 info/about.json 文件中对于使用的 channels 设置配置当前环境的 channels** - - ![image-guide-007.png](images/image-guide-007.png) - ![image-guide-008.png](images/image-guide-008.png) - - ```shell - # 查看 info/about.json 文件中前10行信息[其他包请根据实际情况查看] - tar -xjf /home/KunpengCompute/Download/kallisto-0.48.0-h0d531b0_1.tar.bz2 info/about.json --to-command="head -n 10" - - # 根据上一命令输出的结果增加本地 channels 设置 - # [因 https://repo.anaconda.com/pkgs/main 为 Anaconda 的默认设置项,所以只增加 conda-forge bioconda] - # 有关设置的具体信息可使用 conda config --show 进行查看 - conda config --append channels conda-forge - conda config --append channels bioconda - ``` - -2. **修改 recipe/conda_build_config.yaml 中 linux-64 关键字修改为 linux-aarch64** - - ![image-guide-009.png](images/image-guide-009.png) - - ```shell - # 查看 recipe/conda_build_config.yaml 文件中 target_platform: 的指 - grep 'target_platform:' /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/conda_build_config.yaml - - # 替换 target_platform: linux-64 为 target_platform: linux-aarch64 - sed -i 's/target_platform: linux-64/target_platform: linux-aarch64/g' /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/conda_build_config.yaml - ``` - -3. **将 recipe/meta.yaml 中的构建及运行时所依赖软件包修改为对应的 linux-aarch64 软件包** *[尽量保证所依赖软件包的版本一致,请在 [**ANACONDA.ORG**](https://anaconda.org/) 搜索所需要的软件包]* - - ```shell - # 修改前原始的 meta.yaml - tar -xjf /home/KunpengCompute/Download/kallisto-0.48.0-h0d531b0_1.tar.bz2 info/recipe/meta.yaml --to-command="cat" - ############################################################################################################################# - - # This file created by conda-build 3.21.4 - # meta.yaml template originally from: - # /opt/recipe, last modified Tue Feb 22 19:56:32 2022 - # ------------------------------------------------ - - package: - name: kallisto - version: 0.48.0 - source: - sha256: 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 - url: https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - build: - number: '1' - string: h0d531b0_1 - requirements: - build: - - _libgcc_mutex 0.1 conda_forge - - _openmp_mutex 4.5 1_gnu - - autoconf 2.69 pl5321hd708f79_11 - - automake 1.16.5 pl5321ha770c72_0 - - binutils_impl_linux-64 2.36.1 h193b22a_2 - - binutils_linux-64 2.36 hf3e587d_5 - - bzip2 1.0.8 h7f98852_4 - - c-ares 1.18.1 h7f98852_0 - - ca-certificates 2021.10.8 ha878542_0 - - cmake 3.22.2 h1021d11_0 - - expat 2.4.6 h27087fc_0 - - gcc_impl_linux-64 10.3.0 hf2f2afa_12 - - gcc_linux-64 10.3.0 hc39de41_5 - - gxx_impl_linux-64 10.3.0 hf2f2afa_12 - - gxx_linux-64 10.3.0 h2593f52_5 - - kernel-headers_linux-64 2.6.32 he073ed8_15 - - krb5 1.19.2 h48eae69_3 - - ld_impl_linux-64 2.36.1 hea4e1c9_2 - - libcurl 7.81.0 h494985f_0 - - libedit 3.1.20191231 he28a2e2_2 - - libev 4.33 h516909a_1 - - libgcc-devel_linux-64 10.3.0 he6cfe16_12 - - libgcc-ng 11.2.0 h1d223b6_12 - - libgomp 11.2.0 h1d223b6_12 - - libnghttp2 1.46.0 ha19adfc_0 - - libnsl 2.0.0 h7f98852_0 - - libsanitizer 10.3.0 h26c7422_12 - - libssh2 1.10.0 ha35d2d1_2 - - libstdcxx-devel_linux-64 10.3.0 he6cfe16_12 - - libstdcxx-ng 11.2.0 he4da1e4_12 - - libuv 1.43.0 h7f98852_0 - - libzlib 1.2.11 h36c2ea0_1013 - - lz4-c 1.9.3 h9c3ff4c_1 - - m4 1.4.18 h516909a_1001 - - make 4.3 hd18ef5c_1 - - ncurses 6.3 h9c3ff4c_0 - - openssl 3.0.0 h7f98852_2 - - perl 5.32.1 2_h7f98852_perl5 - - rhash 1.4.1 h7f98852_0 - - sysroot_linux-64 2.12 he073ed8_15 - - tk 8.6.12 h27826a3_0 - - xz 5.2.5 h516909a_1 - - zlib 1.2.11 h36c2ea0_1013 - - zstd 1.5.2 ha95c52a_0 - host: - - _libgcc_mutex 0.1 conda_forge - - _openmp_mutex 4.5 1_gnu - - c-ares 1.18.1 h7f98852_0 - - ca-certificates 2021.10.8 ha878542_0 - - hdf5 1.10.6 nompi_h6a2412b_1114 - - krb5 1.19.2 hcc1bbae_3 - - libcurl 7.81.0 h2574ce0_0 - - libedit 3.1.20191231 he28a2e2_2 - - libev 4.33 h516909a_1 - - libgcc-ng 11.2.0 h1d223b6_12 - - libgfortran-ng 11.2.0 h69a702a_12 - - libgfortran5 11.2.0 h5c6108e_12 - - libgomp 11.2.0 h1d223b6_12 - - libnghttp2 1.46.0 h812cca2_0 - - libssh2 1.10.0 ha56f1ee_2 - - libstdcxx-ng 11.2.0 he4da1e4_12 - - libzlib 1.2.11 h36c2ea0_1013 - - ncurses 6.3 h9c3ff4c_0 - - openssl 1.1.1l h7f98852_0 - - tk 8.6.12 h27826a3_0 - - zlib 1.2.11 h36c2ea0_1013 - run: - - hdf5 >=1.10.6,<1.10.7.0a0 - - libgcc-ng >=10.3.0 - - libstdcxx-ng >=10.3.0 - - libzlib >=1.2.11,<1.3.0a0 - - zlib >=1.2.11,<1.3.0a0 - test: - commands: - - kallisto cite - about: - home: http://pachterlab.github.io/kallisto - license: BSD_2_Clause - summary: Quantifying abundances of transcripts from RNA-Seq data, or more generally - of target sequences using high-throughput sequencing reads. - extra: - copy_test_source_files: true - final: true - identifiers: - - biotools:kallisto - - doi:10.1038/nbt.3519 - skip-lints: - - missing_tests - ``` - - ```shell - # 修改后的 meta.yml - cat /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml - ############################################################################################################################# - - # This file created by conda-build 3.21.4 - # meta.yaml template originally from: - # /opt/recipe, last modified Tue Feb 22 19:56:32 2022 - # ------------------------------------------------ - - package: - name: kallisto - version: 0.48.0 - source: - sha256: 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 - url: https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - build: - number: '1' - string: h0d531b0_1_kp - requirements: - build: - - _libgcc_mutex 0.1 main - - _openmp_mutex 4.5 2_gnu - - autoconf 2.69 pl5262hfd63f10_5 - - automake 1.16.5 pl5321h8af1aa0_0 - - binutils_impl_linux-aarch64 2.36.1 h0d3074b_3 - - binutils_linux-aarch64 2.36 h7854541_10 - - bzip2 1.0.8 hfd63f10_2 - - c-ares 1.18.1 h2f4d8fa_0 - - ca-certificates 2021.10.8 h4fd8a4c_0 - - cmake 3.22.2 hdbbab26_0 - - expat 2.4.6 ha18d298_0 - - gcc_impl_linux-aarch64 10.3.0 ha07e0e6_16 - - gcc_linux-aarch64 10.3.0 h4e3e293_10 - - gxx_impl_linux-aarch64 10.3.0 ha07e0e6_16 - - gxx_linux-aarch64 10.3.0 h72ff769_10 - - kernel-headers_linux-aarch64 4.18.0 h5b4a56d_13 - - krb5 1.19.2 h750e270_4 - - ld_impl_linux-aarch64 2.36.1 h0ab8de2_3 - - libcurl 7.81.0 hbeee725_0 - - libedit 3.1.20191231 hfd63f10_0 - - libev 4.33 hfd63f10_1 - - libgcc-devel_linux-aarch64 10.3.0 h8e480ec_16 - - libgcc-ng 11.2.0 h1234567_0 - - libgomp 11.2.0 h1234567_0 - - libnghttp2 1.46.0 h3bc09fb_0 - - libnsl 2.0.0 hf897c2e_0 - - libsanitizer 10.3.0 h971684a_16 - - libssh2 1.10.0 hd8c4cff_2 - - libstdcxx-devel_linux-aarch64 10.3.0 h8e480ec_16 - - libstdcxx-ng 11.2.0 h1234567_0 - - libuv 1.43.0 hf897c2e_0 - - libzlib 1.2.11 h4e544f5_1014 - - lz4-c 1.9.3 h7c1a80f_0 - - m4 1.4.18 hfd63f10_1 - - make 4.3 h309ac5b_1 - - ncurses 6.3 h2f4d8fa_2 - - openssl 3.0.0 hf897c2e_1 - - perl 5.32.1 2_hf897c2e_perl5 - - rhash 1.4.1 hf897c2e_0 - - sysroot_linux-aarch64 2.17 h43d7e78_13 - - tk 8.6.12 hd8af866_0 - - xz 5.2.5 h2f4d8fa_1 - - zlib 1.2.11 h4e544f5_1014 - - zstd 1.5.2 haad177d_1 - host: - - _libgcc_mutex 0.1 main - - _openmp_mutex 4.5 2_gnu - - c-ares 1.18.1 h2f4d8fa_0 - - ca-certificates 2021.10.8 h4fd8a4c_0 - - hdf5 1.10.6 h702ddfa_0 - - krb5 1.19.2 h7c456eb_4 - - libcurl 7.81.0 hcafe9da_0 - - libedit 3.1.20191231 hfd63f10_0 - - libev 4.33 hfd63f10_1 - - libgcc-ng 11.2.0 h1234567_0 - - libgfortran-ng 11.2.0 h6e398d7_0 - - libgfortran5 11.2.0 h1234567_0 - - libgomp 11.2.0 h1234567_0 - - libnghttp2 1.46.0 hb87466c_0 - - libssh2 1.10.0 h1ab2c7b_2 - - libstdcxx-ng 11.2.0 h1234567_0 - - libzlib 1.2.11 h4e544f5_1014 - - ncurses 6.3 h2f4d8fa_2 - - openssl 1.1.1l h2f4d8fa_0 - - tk 8.6.12 hd8af866_0 - - zlib 1.2.11 h4e544f5_1014 - run: - - hdf5 >=1.10.6,<1.10.7.0a0 - - libgcc-ng >=10.3.0 - - libstdcxx-ng >=10.3.0 - - libzlib >=1.2.11,<1.3.0a0 - - zlib >=1.2.11,<1.3.0a0 - test: - commands: - - kallisto cite - about: - home: http://pachterlab.github.io/kallisto - license: BSD_2_Clause - summary: Quantifying abundances of transcripts from RNA-Seq data, or more generally - of target sequences using high-throughput sequencing reads. - extra: - copy_test_source_files: true - final: true - identifiers: - - biotools:kallisto - - doi:10.1038/nbt.3519 - skip-lints: - - missing_tests - ``` - - ![image-guide-010.png](images/image-guide-010.png) - ![image-guide-011.png](images/image-guide-011.png) - - ```shell - # meta.yml 修改前后不同项对比[左边为修改前,右边为修改后] - diff -y --suppress-common-lines /home/KunpengCompute/Download/recipe/meta.yaml /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml - ############################################################################################################################# - - string: h0d531b0_1 | string: h0d531b0_1_kp - - _libgcc_mutex 0.1 conda_forge | - _libgcc_mutex 0.1 main - - _openmp_mutex 4.5 1_gnu | - _openmp_mutex 4.5 2_gnu - - autoconf 2.69 pl5321hd708f79_11 | - autoconf 2.69 pl5262hfd63f10_5 - - automake 1.16.5 pl5321ha770c72_0 | - automake 1.16.5 pl5321h8af1aa0_0 - - binutils_impl_linux-64 2.36.1 h193b22a_2 | - binutils_impl_linux-aarch64 2.36.1 h0d3074b_3 - - binutils_linux-64 2.36 hf3e587d_5 | - binutils_linux-aarch64 2.36 h7854541_10 - - bzip2 1.0.8 h7f98852_4 | - bzip2 1.0.8 hfd63f10_2 - - c-ares 1.18.1 h7f98852_0 | - c-ares 1.18.1 h2f4d8fa_0 - - ca-certificates 2021.10.8 ha878542_0 | - ca-certificates 2021.10.8 h4fd8a4c_0 - - cmake 3.22.2 h1021d11_0 | - cmake 3.22.2 hdbbab26_0 - - expat 2.4.6 h27087fc_0 | - expat 2.4.6 ha18d298_0 - - gcc_impl_linux-64 10.3.0 hf2f2afa_12 | - gcc_impl_linux-aarch64 10.3.0 ha07e0e6_16 - - gcc_linux-64 10.3.0 hc39de41_5 | - gcc_linux-aarch64 10.3.0 h4e3e293_10 - - gxx_impl_linux-64 10.3.0 hf2f2afa_12 | - gxx_impl_linux-aarch64 10.3.0 ha07e0e6_16 - - gxx_linux-64 10.3.0 h2593f52_5 | - gxx_linux-aarch64 10.3.0 h72ff769_10 - - kernel-headers_linux-64 2.6.32 he073ed8_15 | - kernel-headers_linux-aarch64 4.18.0 h5b4a56d_13 - - krb5 1.19.2 h48eae69_3 | - krb5 1.19.2 h750e270_4 - - ld_impl_linux-64 2.36.1 hea4e1c9_2 | - ld_impl_linux-aarch64 2.36.1 h0ab8de2_3 - - libcurl 7.81.0 h494985f_0 | - libcurl 7.81.0 hbeee725_0 - - libedit 3.1.20191231 he28a2e2_2 | - libedit 3.1.20191231 hfd63f10_0 - - libev 4.33 h516909a_1 | - libev 4.33 hfd63f10_1 - - libgcc-devel_linux-64 10.3.0 he6cfe16_12 | - libgcc-devel_linux-aarch64 10.3.0 h8e480ec_16 - - libgcc-ng 11.2.0 h1d223b6_12 | - libgcc-ng 11.2.0 h1234567_0 - - libgomp 11.2.0 h1d223b6_12 | - libgomp 11.2.0 h1234567_0 - - libnghttp2 1.46.0 ha19adfc_0 | - libnghttp2 1.46.0 h3bc09fb_0 - - libnsl 2.0.0 h7f98852_0 | - libnsl 2.0.0 hf897c2e_0 - - libsanitizer 10.3.0 h26c7422_12 | - libsanitizer 10.3.0 h971684a_16 - - libssh2 1.10.0 ha35d2d1_2 | - libssh2 1.10.0 hd8c4cff_2 - - libstdcxx-devel_linux-64 10.3.0 he6cfe16_12 | - libstdcxx-devel_linux-aarch64 10.3.0 h8e480ec_16 - - libstdcxx-ng 11.2.0 he4da1e4_12 | - libstdcxx-ng 11.2.0 h1234567_0 - - libuv 1.43.0 h7f98852_0 | - libuv 1.43.0 hf897c2e_0 - - libzlib 1.2.11 h36c2ea0_1013 | - libzlib 1.2.11 h4e544f5_1014 - - lz4-c 1.9.3 h9c3ff4c_1 | - lz4-c 1.9.3 h7c1a80f_0 - - m4 1.4.18 h516909a_1001 | - m4 1.4.18 hfd63f10_1 - - make 4.3 hd18ef5c_1 | - make 4.3 h309ac5b_1 - - ncurses 6.3 h9c3ff4c_0 | - ncurses 6.3 h2f4d8fa_2 - - openssl 3.0.0 h7f98852_2 | - openssl 3.0.0 hf897c2e_1 - - perl 5.32.1 2_h7f98852_perl5 | - perl 5.32.1 2_hf897c2e_perl5 - - rhash 1.4.1 h7f98852_0 | - rhash 1.4.1 hf897c2e_0 - - sysroot_linux-64 2.12 he073ed8_15 | - sysroot_linux-aarch64 2.17 h43d7e78_13 - - tk 8.6.12 h27826a3_0 | - tk 8.6.12 hd8af866_0 - - xz 5.2.5 h516909a_1 | - xz 5.2.5 h2f4d8fa_1 - - zlib 1.2.11 h36c2ea0_1013 | - zlib 1.2.11 h4e544f5_1014 - - zstd 1.5.2 ha95c52a_0 | - zstd 1.5.2 haad177d_1 - - _libgcc_mutex 0.1 conda_forge | - _libgcc_mutex 0.1 main - - _openmp_mutex 4.5 1_gnu | - _openmp_mutex 4.5 2_gnu - - c-ares 1.18.1 h7f98852_0 | - c-ares 1.18.1 h2f4d8fa_0 - - ca-certificates 2021.10.8 ha878542_0 | - ca-certificates 2021.10.8 h4fd8a4c_0 - - hdf5 1.10.6 nompi_h6a2412b_1114 | - hdf5 1.10.6 h702ddfa_0 - - krb5 1.19.2 hcc1bbae_3 | - krb5 1.19.2 h7c456eb_4 - - libcurl 7.81.0 h2574ce0_0 | - libcurl 7.81.0 hcafe9da_0 - - libedit 3.1.20191231 he28a2e2_2 | - libedit 3.1.20191231 hfd63f10_0 - - libev 4.33 h516909a_1 | - libev 4.33 hfd63f10_1 - - libgcc-ng 11.2.0 h1d223b6_12 | - libgcc-ng 11.2.0 h1234567_0 - - libgfortran-ng 11.2.0 h69a702a_12 | - libgfortran-ng 11.2.0 h6e398d7_0 - - libgfortran5 11.2.0 h5c6108e_12 | - libgfortran5 11.2.0 h1234567_0 - - libgomp 11.2.0 h1d223b6_12 | - libgomp 11.2.0 h1234567_0 - - libnghttp2 1.46.0 h812cca2_0 | - libnghttp2 1.46.0 hb87466c_0 - - libssh2 1.10.0 ha56f1ee_2 | - libssh2 1.10.0 h1ab2c7b_2 - - libstdcxx-ng 11.2.0 he4da1e4_12 | - libstdcxx-ng 11.2.0 h1234567_0 - - libzlib 1.2.11 h36c2ea0_1013 | - libzlib 1.2.11 h4e544f5_1014 - - ncurses 6.3 h9c3ff4c_0 | - ncurses 6.3 h2f4d8fa_2 - - openssl 1.1.1l h7f98852_0 | - openssl 1.1.1l h2f4d8fa_0 - - tk 8.6.12 h27826a3_0 | - tk 8.6.12 hd8af866_0 - - zlib 1.2.11 h36c2ea0_1013 | - zlib 1.2.11 h4e544f5_1014 - - ``` - -### 三、使用 Conda-build 进行编译 - -```shell -# 执行构建 -conda build /home/KunpengCompute/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe -``` - -### 四、验证迁移后的软件包 -![image-guide-012.png](images/image-guide-012.png) - -![image-guide-013.png](images/image-guide-013.png) -![image-guide-014.png](images/image-guide-014.png) -![image-guide-015.png](images/image-guide-015.png) -![image-guide-016.png](images/image-guide-016.png) - -```shell -# 产看构建成功后本地仓库的软件包 -ls -l /root/anaconda3/conda-bld/linux-aarch64/ - -# 创建一个虚拟环境 -conda create -n kallisto -# 开启创建的虚拟环境 -conda activate kallisto -# 安装构建成功的 kallisto 软件包 -conda install -c local kallisto -# 执行基本的测试命令 -kallisto version -kallisto cite -kallisto -``` - -相关资源连接: - -conda 相关文档: https://docs.conda.io/en/latest/ - -conda: https://docs.conda.io/projects/conda/en/latest/ - -conda-build: https://docs.conda.io/projects/conda-build/en/latest/ - -ANACONDA.ORG: https://anaconda.org/ - -kallisto: https://pachterlab.github.io/kallisto/ - -pachterlab/kallisto GitHub: https://github.com/pachterlab/kallisto - -kallisto anaconda package: https://anaconda.org/bioconda/kallisto diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda.md" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda.md" deleted file mode 100644 index 262bbcd9d8cc374b1c1248e13044a93f634e648a..0000000000000000000000000000000000000000 --- "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda.md" +++ /dev/null @@ -1,185 +0,0 @@ -# Linux环境中安装Anaconda - -> 以下安装方式仅针对于单用户安装方式 -> -> 当前安装环境如下图 -> -> ![image-021.png](images/image-021.png) -> -> **[安装 Anaconda 的系统要求](https://docs.anaconda.com/anaconda/install/#)** - - -[TOC] - -## 一、下载 Anaconda - -​ **Anaconda 下载来源** -​ (1)从官方进行下载: https://www.anaconda.com/products/distribution#Downloads -​ (2)从官方安装包仓库下载: https://repo.anaconda.com/archive/ -​ (3)从清华镜像的安装包仓库下载: https://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/ -​ 【请根据自己的实际需求选择对应的版本】 - -1. **使用 curl下载** - ![image-001.png](images/image-001.png) - - ```shell - curl -o ~/Download/Anaconda3-2022.05-Linux-aarch64.sh https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-aarch64.sh - ``` - -2. **使用 wget下载** - ![image-002.png](images/image-002.png) - - ```shell - wget -O ~/Download/Anaconda3-2022.05-Linux-aarch64.sh https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-aarch64.sh - ``` - -3. **使用 [HTTPie](https://httpie.io/)下载** *[请确保您已安装HTTPie]* - - ![image-003.png](images/image-003.png) - - ```shell - # 在 openEuler release 20.03 (LTS-SP3) 上安装 HTTPie - # 请确保您拥有 Python 3.7 或更新版本 ( python --version) - python3 -m pip install --upgrade pip - python3 -m pip install wheel - python3 -m pip install httpie - - # 下载 Anaconda3-2022.05-Linux-aarch64.sh - http --default-scheme=https --print b --download --continue --output ~/Download/Anaconda3-2022.05-Linux-aarch64.sh https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-aarch64.sh - ``` - -## 二、验证下载的文件 - -1. **使用 md5sum 进行文件校验** - - ![image-004.png](images/image-004.png) - - ```shell - md5sum ~/Download/Anaconda3-2022.05-Linux-aarch64.sh | grep 7e822f5622fa306c0aa42430ba884454 - ``` - -## 三、如果需要使用 Anaconda 的 GUI 模式建议安装以下依赖 [为避免后续不必要的错误提示建议执行本步骤操作] - -1. **安装所需要的 GUI 依赖** - - ```shell - # 当前命令仅适用于 RHEL Fedora CentOS openEuler - dnf install libXcomposite libXcursor libXi libXtst libXrandr alsa-lib mesa-libEGL libXdamage mesa-libGL libXScrnSaver gtk3 -y - ``` - - [其他 Linux 发行版的安装方式](https://docs.anaconda.com/anaconda/install/linux/#prerequisites) - -## 四、安装 Anaconda - - 1. **执行安装 shell** - - ![image-005.png](images/image-005.png) - - ```shell - bash ~/Download/Anaconda3-2021.11-Linux-aarch64.sh - ``` - - 2. **确认阅览协议** *[敲击 ENTER]* - - ![image-006.png](images/image-006.png) - - 3. **确认签署协议** *[敲击 1到2次 f ,直至出现 Do you accept the license terms? [yes|no] 时,输入 yes 并敲击 ENTER]* - - ![image-007.png](images/image-007.png) - - 4. **确认安装** *[敲击 ENTER]* - - ![image-008.png](images/image-008.png) - - 5. **初始化当前用户默认shell的conda环境配置** *[输入 yes 并敲击 ENTER]* - - ![image-009.png](images/image-009.png) - ![image-010.png](images/image-010.png) - -## 五、验证安装 - - 1. **执行 conda 命令验证安装** - - ![image-011.png](images/image-011.png) - - ```shell - conda --version - ``` - -## 六、更新 Anaconda & conda - - 1. **执行更新命令** - - ![image-012.png](images/image-012.png) - - ```shell - conda update --all - ``` - - 2. **确认更新** *[输入 y 并敲击 ENTER]* - - ![image-013.png](images/image-013.png) - - 3. **更新完成** - - ![image-014.png](images/image-014.png) - -## 七、扩展配置 - - 1. **进行初始设置** - - ![image-015.png](images/image-015.png) - - ```shell - conda config --set auto_activate_base False - ``` - - ```shell - conda config --set auto_update_conda False - ``` - - ```shell - conda config --set show_channel_urls True - ``` - *有关 conda 的其他配置请查阅以下官方文档:* - - [Using the .condarc conda configuration file]: https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/use-condarc.html - [Conda configuration]: https://docs.conda.io/projects/conda/en/latest/configuration.html - - 1. **使用 fish shell 操作 conda 命令** *[fish 对于 conda 命令的自动补全提示最好]* `推荐使用` - - ```shell - # 安装 fish - sudo dnf install fish -y - ``` - - ```shell - # 初始化 fish 中 conda 的环境变量 - conda init fish - ``` - - ![image-016.png](images/image-016.png) - - ![image-017.png](images/image-017.png) - - ![image-018.png](images/image-018.png) - - ![image-019.png](images/image-019.png) - - ```shell - ## 如果你更愿意使用 zsh 请执行以下命令 - # 安装 fish - sudo dnf install zsh -y - # 初始化 zsh 中 conda 的环境变量 - conda init zsh - ``` - - ![image-020.png](images/image-020.png) - -相关资源连接: - -Anaconda 官网: https://www.anaconda.com/ - -Anaconda Packages repository: https://repo.anaconda.com/pkgs/ - -Anaconda Documentation: https://docs.anaconda.com/ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-001.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-001.png" deleted file mode 100644 index ce6d46de3fd8a04df37b57f4ed8cf314da8dd8e1..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-001.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-002.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-002.png" deleted file mode 100644 index c02314256d5aba60273dd7fb336ac9b022edfa58..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-002.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-003.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-003.png" deleted file mode 100644 index 8d134a729766dabc3c4d86eedf3ca1da408ee3f8..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-003.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-004.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-004.png" deleted file mode 100644 index 4e46cbf6a85f94cc1b0dbab35828ba516245c8fd..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-004.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-005.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-005.png" deleted file mode 100644 index cc4a1889e183ed7bbfc2248f88bbb9c68d878ade..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-005.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-006.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-006.png" deleted file mode 100644 index 4fa93ff5a71dadc1fbb73c4c751ecb389e6a5fc2..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-006.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-007.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-007.png" deleted file mode 100644 index 0df87761de0550eb34a95916891ada734ee1d33e..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-007.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-008.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-008.png" deleted file mode 100644 index 758d3903989aceb985c38c02d2ff5a62cf3081d9..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-008.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-009.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-009.png" deleted file mode 100644 index 5e2c841e54f9de371d7112a4631557f52d1dc37e..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-009.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-010.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-010.png" deleted file mode 100644 index c61bcb98b21997862415b44e55fdf50477a1c4b8..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-010.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-011.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-011.png" deleted file mode 100644 index 64616f53bb93567c0da7fb38a0bbc3ceb0ecc4df..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-011.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-012.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-012.png" deleted file mode 100644 index 9cb1edc9ecb87144ae6435c5d68ccdafe4aa13b7..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-012.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-013.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-013.png" deleted file mode 100644 index 160deece5879e84b83d0f3311cfd2d4caf4a21f6..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-013.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-014.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-014.png" deleted file mode 100644 index b902f1afafb5614e2e292b3fecf0ac238b9bdaeb..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-014.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-015.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-015.png" deleted file mode 100644 index db11e593e1ac709b1991eedcbc6f0187a351421b..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-015.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-016.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-016.png" deleted file mode 100644 index e3109a452ed85e49576872ffa4e34fe9531ce0dc..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-016.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-017.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-017.png" deleted file mode 100644 index f5ee21fdf73f95bb6a3e30e493584498a95ef67c..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-017.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-018.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-018.png" deleted file mode 100644 index 40df9021ba7a66533185fdffea95c6676f20afdc..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-018.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-019.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-019.png" deleted file mode 100644 index 5ef086c086586ff47781e159e4714e964a7a407a..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-019.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-020.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-020.png" deleted file mode 100644 index 4309034254775db6e4e2c8cfb425f6209b5903b7..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-020.png" and /dev/null differ diff --git "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-021.png" "b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-021.png" deleted file mode 100644 index f543f367a27e3ef911337d7ec689ac2e9f241e19..0000000000000000000000000000000000000000 Binary files "a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/Linux\347\216\257\345\242\203\344\270\255\345\256\211\350\243\205Anaconda/images/image-021.png" and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-001.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-001.png deleted file mode 100644 index 8e7baa15d1cfa59280b1dcd855d86053db9ae2fd..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-001.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-002.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-002.png deleted file mode 100644 index 0f5aa59de370d63ea8cd2829b8583915b7b451cb..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-002.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-003.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-003.png deleted file mode 100644 index db8383ac0003c07767dde1f76b0741a1f6b6a3a5..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-003.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-004.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-004.png deleted file mode 100644 index a5c42fe0f1fcf40ea9b6cd04a6175efa330147a0..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-004.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-005.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-005.png deleted file mode 100644 index cba050aa2a330d0d2fc5434dcdb43d9c111eea6e..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-005.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-006.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-006.png deleted file mode 100644 index 0c2e2227fba61841f7b08bf7a4d9d8bea3169be7..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-006.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-007.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-007.png deleted file mode 100644 index 6f525b87a10218215bc6f7bcda57c86dc44739d4..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-007.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-008.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-008.png deleted file mode 100644 index 702468d606823ebf6254055a0b21bd37fc1dc50f..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-008.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-009.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-009.png deleted file mode 100644 index dd186f9cbdc90a58acfadd2818c1dc3c95307726..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-009.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-010.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-010.png deleted file mode 100644 index 2b5ceb42c516438fd6dd84251206548eaa15ac3a..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-010.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-011.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-011.png deleted file mode 100644 index da821d8dcb43c43db4550eb69ec0773fc8e180a4..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-011.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-012.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-012.png deleted file mode 100644 index 502e00b2c644423ab8ea33726d609724b838c346..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-012.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-013.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-013.png deleted file mode 100644 index 515bca9de5ac1fce9b91d023de62500224beed82..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-013.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-014.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-014.png deleted file mode 100644 index 4dd4ae86f879e93bde20762d74790dc08deb011e..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-014.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-015.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-015.png deleted file mode 100644 index 0104173072dfefddfbc0c65105b38dac5ad15194..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-015.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-016.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-016.png deleted file mode 100644 index 4c8beec6f2434e45b9a8f91f25e9137629138904..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-016.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-001.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-001.png deleted file mode 100644 index 46eb5c0b3a281a2ae9a8fce7adf06dc33372f26d..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-001.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-002.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-002.png deleted file mode 100644 index 69ac09189ffc69792c8933242d047af498b691bc..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-002.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-003.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-003.png deleted file mode 100644 index 906d241c2dd99d1c100c77e7d55285ad3fb7c44e..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-003.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-004.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-004.png deleted file mode 100644 index 6a43a031727d98d2074f2ac59ccefe1575275909..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-004.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-005.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-005.png deleted file mode 100644 index 99c6909339dcba30ab263fb8e3cb5a119c6320d8..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-005.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-006.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-006.png deleted file mode 100644 index 4df26f9901d42148202b03ba31a4b71978ec0dc5..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-006.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-007.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-007.png deleted file mode 100644 index 9ee3e906688141d7d9900e17152d57115bf3c26d..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-007.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-008.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-008.png deleted file mode 100644 index 3bce178a864d4dfc71e356536f03b647ecfce53b..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-008.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-009.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-009.png deleted file mode 100644 index 96fb5ac06158e5ccb6f5a93d49c8f695ef797a1a..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-009.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-010.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-010.png deleted file mode 100644 index cbd78599f0dc2d07a20be8ee6a6f55fdd33700e9..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-010.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-011.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-011.png deleted file mode 100644 index 84669c76da646c7c2329bf9e5fbf7927384d46b0..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-011.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-012.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-012.png deleted file mode 100644 index 0764c8079364ce57de3af733e2e88a6a47d04313..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-012.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-013.png b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-013.png deleted file mode 100644 index 024d431ae68eaa5dd63998d7af2d238f623d2011..0000000000000000000000000000000000000000 Binary files a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-report-013.png and /dev/null differ diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/build.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/build.sh deleted file mode 100644 index 6c2dd25276e96a04432f791c4eb210e4471440a8..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/build.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash - -cd ext/htslib -autoreconf -cd ../.. - - -mkdir -p $PREFIX/bin - -mkdir -p build -cd build - -cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX .. -DUSE_HDF5=ON -make -make install diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/conda_build_config.yaml b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/conda_build_config.yaml deleted file mode 100644 index 4c754a45dcc1b0b9ccde417785938d5de41e634f..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/conda_build_config.yaml +++ /dev/null @@ -1,404 +0,0 @@ -CONDA_BUILD_SYSROOT: '' -MACOSX_DEPLOYMENT_TARGET: '10.9' -VERBOSE_AT: V=1 -VERBOSE_CM: VERBOSE=1 -_libgcc_mutex: 0.1 conda_forge -abseil_cpp: '20210324.2' -alsa_lib: 1.2.3 -antic: '0.2' -arb: '2.21' -arpack: '3.7' -arrow_cpp: 6.0.1 -assimp: '5.2' -aws_c_auth: 0.6.10 -aws_c_cal: 0.5.12 -aws_c_common: 0.6.19 -aws_c_event_stream: 0.2.7 -aws_c_http: 0.6.10 -aws_c_io: 0.10.17 -aws_c_mqtt: 0.7.10 -aws_c_s3: 0.1.32 -aws_c_sdkutils: 0.1.1 -aws_checksums: 0.1.12 -aws_crt_cpp: 0.17.15 -aws_sdk_cpp: 1.9.160 -bamtools: 2.5.1 -blas_impl: openblas -boost: 1.74.0 -boost_cpp: 1.74.0 -bzip2: '1' -c_compiler: gcc -c_compiler_version: '10' -cairo: '1.16' -capnproto: 0.9.1 -ccr: '1.3' -cdt_name: cos6 -cfitsio: 4.0.0 -cgo_compiler: go-cgo -channel_sources: conda-forge,bioconda,defaults -channel_targets: bioconda main -coin_or_cbc: '2.10' -coin_or_cgl: '0.60' -coin_or_clp: '1.17' -coin_or_osi: '0.108' -coin_or_utils: '2.11' -coincbc: '2.10' -cpu_optimization_target: nocona -cran_mirror: https://cran.r-project.org -cuda_compiler: nvcc -cuda_compiler_version: None -cudnn: undefined -curl: '7' -cutensor: '1' -cxx_compiler: gxx -cxx_compiler_version: '10' -davix: '0.8' -dbus: '1' -exiv2: '0.27' -expat: '2' -extend_keys: -- pin_run_as_build -- ignore_version -- ignore_build_only_deps -- extend_keys -ffmpeg: '4.3' -fftw: '3' -flann: 1.9.1 -fmt: '8' -fontconfig: '2.13' -fortran_compiler: gfortran -fortran_compiler_version: '10' -freetype: '2' -gct: 6.2.1629922860 -gdal: '3.4' -gdk_pixbuf: '2' -geos: 3.10.2 -geotiff: '1.7' -gf2x: '1.3' -gfal2: '2.20' -gflags: '2.2' -giflib: '5.2' -glew: '2.1' -glib: '2' -glog: '0.5' -glpk: '4.65' -gmp: '6' -gnuradio_core: 3.10.0 -go_compiler: go-nocgo -google_cloud_cpp: '1.35' -google_cloud_cpp_common: 0.25.0 -googleapis_cpp: '0.10' -graphviz: '2.47' -grpc_cpp: '1.43' -gsl: '2.7' -gsoap: 2.8.119 -gst_plugins_base: '1.18' -gstreamer: '1.18' -harfbuzz: '3' -hdf4: '4.2' -hdf5: 1.10.6 -htslib: '1.14' -icu: '69' -ignore_build_only_deps: -- python -- numpy -ipopt: '3.14' -isl: '0.22' -jasper: '2' -jpeg: '9' -json_c: '0.15' -jsoncpp: 1.9.5 -kealib: '1.4' -krb5: '1.19' -libarchive: '3.5' -libblas: 3.8 *netlib -libblitz: 1.0.2 -libcblas: 3.8 *netlib -libcint: '5.1' -libcrc32c: '1.1' -libcurl: '7' -libdap4: 3.20.6 -libdeflate: '1.10' -libeantic: '1' -libevent: 2.1.10 -libexactreal: '2' -libffi: '3.3' -libflatsurf: '3' -libflint: '2.8' -libgdal: '3.4' -libgit2: '1.3' -libhugetlbfs: '2' -libhwy: '0.15' -libiconv: '1.16' -libiio: '0' -libintervalxt: '3' -libjpeg_turbo: '2' -libkml: '1.3' -liblapack: 3.8 *netlib -liblapacke: 3.8 *netlib -libmatio: 1.5.21 -libmicrohttpd: '0.9' -libnetcdf: 4.8.1 -libopencv: 4.5.5 -libpcap: '1.10' -libpng: '1.6' -libprotobuf: '3.18' -librdkafka: '1.7' -librsvg: '2' -libsecret: '0.18' -libspatialindex: 1.9.3 -libssh2: '1' -libsvm: '3.21' -libthrift: 0.15.0 -libtiff: '4' -libunwind: '1.6' -libuuid: '2' -libv8: 8.9.83 -libvips: '8' -libwebp: '1' -libwebp_base: '1' -libxml2: '2.9' -libxsmm: '1' -libzip: '1' -log4cxx: 0.11.0 -lua: '5' -lz4_c: 1.9.3 -lzo: '2' -metis: '5.1' -mimalloc: 2.0.2 -mkl: '2022' -mkl_devel: '2022' -mpfr: '4' -mpich: '3' -mumps_mpi: '5.2' -mumps_seq: '5.2' -nccl: '2' -ncurses: '6' -netcdf_cxx4: '4.3' -netcdf_fortran: '4.5' -nettle: '3.7' -nlopt: '2.7' -nodejs: '16' -nspr: '4' -nss: '3' -ntl: 11.4.3 -numpy: 1.16.* -occt: '7.5' -openblas: 0.3.* -openexr: '2.5' -openjpeg: '2.4' -openmpi: '4' -openssl: 1.1.1 -openturns: '1.18' -orc: 1.7.3 -pango: '1.48' -pari: 2.13.* *_pthread -pcre: '8' -pcre2: '10.37' -perl: 5.32.1 -petsc: '3.15' -petsc4py: '3.15' -pin_run_as_build: - python: - min_pin: x.x - max_pin: x.x - r-base: - max_pin: x.x - min_pin: x.x - arpack: - max_pin: x.x.x - boost: - max_pin: x.x.x - boost-cpp: - max_pin: x.x.x - bzip2: - max_pin: x - cairo: - max_pin: x.x - curl: - max_pin: x - dbus: - max_pin: x - fftw: - max_pin: x - flann: - max_pin: x.x.x - fontconfig: - max_pin: x - freetype: - max_pin: x - gdal: - max_pin: x.x - geotiff: - max_pin: x.x.x - glew: - max_pin: x.x - glpk: - max_pin: x.x - gmp: - max_pin: x - graphviz: - max_pin: x - harfbuzz: - max_pin: x - hdf4: - max_pin: x.x - isl: - max_pin: x.x - jasper: - max_pin: x - jpeg: - max_pin: x - libjpeg_turbo: - max_pin: x - json-c: - max_pin: x.x - jsoncpp: - max_pin: x.x.x - kealib: - max_pin: x.x - krb5: - max_pin: x.x - libblitz: - max_pin: x.x - libcurl: - max_pin: x - libevent: - max_pin: x.x.x - libffi: - max_pin: x.x - libgdal: - max_pin: x.x - libiconv: - max_pin: x.x - libkml: - max_pin: x.x - libpng: - max_pin: x.x - librsvg: - max_pin: x - libsvm: - max_pin: x.x - libtiff: - max_pin: x - libxml2: - max_pin: x.x - libuuid: - max_pin: x - lz4-c: - max_pin: x.x.x - lzo: - max_pin: x - metis: - max_pin: x.x - mpfr: - max_pin: x - netcdf-cxx4: - max_pin: x.x - netcdf-fortran: - max_pin: x.x - nettle: - max_pin: x.x - nlopt: - max_pin: x.x.x - nss: - max_pin: x - nspr: - max_pin: x - occt: - max_pin: x.x - openturns: - max_pin: x.x - openjpeg: - max_pin: x.x - pango: - max_pin: x.x - poppler: - max_pin: x.x - qt: - max_pin: x.x - qtkeychain: - max_pin: x.x - readline: - max_pin: x - sox: - max_pin: x.x.x - sqlite: - max_pin: x - tk: - max_pin: x.x - tiledb: - max_pin: x.x - vlfeat: - max_pin: x.x.x - vtk: - max_pin: x.x.x - xz: - max_pin: x.x - zeromq: - max_pin: x.x - zlib: - max_pin: x.x - htslib: - max_pin: x.x - bamtools: - max_pin: x.x.x -pixman: '0' -poco: 1.11.1 -poppler: '22.01' -proj: 8.2.1 -ptscotch: 6.0.9 -pybind11_abi: '4' -python: 2.7.* *_cpython -python_impl: cpython -qt: '5.12' -qtkeychain: '0.12' -r_base: 4.1.* -re2: 2022.02.01 -readline: '8' -rocksdb: '6.10' -root_base: 6.24.6 -ruby: '2.5' -rust_compiler: rust -s2n: 1.3.6 -scotch: 6.0.9 -singular: 4.2.0.p3 -slepc: '3.15' -slepc4py: '3.15' -snappy: '1' -soapysdr: '0.8' -sox: 14.4.2 -spdlog: '1.9' -sqlite: '3' -suitesparse: '5' -superlu_dist: 7.1.1 -target_goarch: amd64 -target_gobin: ${PREFIX}/bin/ -target_goexe: '' -target_goos: linux -target_platform: linux-aarch64 -tbb: '2020' -tbb_devel: '2020' -thrift_cpp: 0.15.0 -tiledb: '2.6' -tinyxml2: '9' -tk: '8.6' -uhd: 4.1.0 -vlfeat: 0.9.20 -volk: '2.5' -vtk: 9.0.1 -x264: 1!161.* -xerces_c: '3.2' -xrootd: '5' -xz: '5.2' -zeromq: 4.3.4 -zip_keys: -- - c_compiler_version - - cxx_compiler_version - - fortran_compiler_version -- - python - - numpy - - python_impl -zlib: '1.2' -zlib_ng: '2.0' -zstd: '1.5' diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml deleted file mode 100644 index 24bc1d936e5d6be73393942f057bb06913da8ebf..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml +++ /dev/null @@ -1,104 +0,0 @@ -# This file created by conda-build 3.21.4 -# meta.yaml template originally from: -# /opt/recipe, last modified Tue Feb 22 19:56:32 2022 -# ------------------------------------------------ - -package: - name: kallisto - version: 0.48.0 -source: - sha256: 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 - url: https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz -build: - number: '1' - string: h0d531b0_1 -requirements: - build: - - _libgcc_mutex 0.1 main - - _openmp_mutex 4.5 2_gnu - - autoconf 2.69 pl5262hfd63f10_5 - - automake 1.16.5 pl5321h8af1aa0_0 - - binutils_impl_linux-aarch64 2.36.1 h0d3074b_3 - - binutils_linux-aarch64 2.36 h7854541_10 - - bzip2 1.0.8 hfd63f10_2 - - c-ares 1.18.1 h2f4d8fa_0 - - ca-certificates 2021.10.8 h4fd8a4c_0 - - cmake 3.22.2 hdbbab26_0 - - expat 2.4.6 ha18d298_0 - - gcc_impl_linux-aarch64 10.3.0 ha07e0e6_16 - - gcc_linux-aarch64 10.3.0 h4e3e293_10 - - gxx_impl_linux-aarch64 10.3.0 ha07e0e6_16 - - gxx_linux-aarch64 10.3.0 h72ff769_10 - - kernel-headers_linux-aarch64 4.18.0 h5b4a56d_13 - - krb5 1.19.2 h750e270_4 - - ld_impl_linux-aarch64 2.36.1 h0ab8de2_3 - - libcurl 7.81.0 hbeee725_0 - - libedit 3.1.20191231 hfd63f10_0 - - libev 4.33 hfd63f10_1 - - libgcc-devel_linux-aarch64 10.3.0 h8e480ec_16 - - libgcc-ng 11.2.0 h1234567_0 - - libgomp 11.2.0 h1234567_0 - - libnghttp2 1.46.0 h3bc09fb_0 - - libnsl 2.0.0 hf897c2e_0 - - libsanitizer 10.3.0 h971684a_16 - - libssh2 1.10.0 hd8c4cff_2 - - libstdcxx-devel_linux-aarch64 10.3.0 h8e480ec_16 - - libstdcxx-ng 11.2.0 h1234567_0 - - libuv 1.43.0 hf897c2e_0 - - libzlib 1.2.11 h4e544f5_1014 - - lz4-c 1.9.3 h7c1a80f_0 - - m4 1.4.18 hfd63f10_1 - - make 4.3 h309ac5b_1 - - ncurses 6.3 h2f4d8fa_2 - - openssl 3.0.0 hf897c2e_1 - - perl 5.32.1 2_hf897c2e_perl5 - - rhash 1.4.1 hf897c2e_0 - - sysroot_linux-aarch64 2.17 h43d7e78_13 - - tk 8.6.12 hd8af866_0 - - xz 5.2.5 h2f4d8fa_1 - - zlib 1.2.11 h4e544f5_1014 - - zstd 1.5.2 haad177d_1 - host: - - _libgcc_mutex 0.1 main - - _openmp_mutex 4.5 2_gnu - - c-ares 1.18.1 h2f4d8fa_0 - - ca-certificates 2021.10.8 h4fd8a4c_0 - - hdf5 1.10.6 h702ddfa_0 - - krb5 1.19.2 h7c456eb_4 - - libcurl 7.81.0 hcafe9da_0 - - libedit 3.1.20191231 hfd63f10_0 - - libev 4.33 hfd63f10_1 - - libgcc-ng 11.2.0 h1234567_0 - - libgfortran-ng 11.2.0 h6e398d7_0 - - libgfortran5 11.2.0 h1234567_0 - - libgomp 11.2.0 h1234567_0 - - libnghttp2 1.46.0 hb87466c_0 - - libssh2 1.10.0 h1ab2c7b_2 - - libstdcxx-ng 11.2.0 h1234567_0 - - libzlib 1.2.11 h4e544f5_1014 - - ncurses 6.3 h2f4d8fa_2 - - openssl 1.1.1l h2f4d8fa_0 - - tk 8.6.12 hd8af866_0 - - zlib 1.2.11 h4e544f5_1014 - run: - - hdf5 >=1.10.6,<1.10.7.0a0 - - libgcc-ng >=10.3.0 - - libstdcxx-ng >=10.3.0 - - libzlib >=1.2.11,<1.3.0a0 - - zlib >=1.2.11,<1.3.0a0 -test: - commands: - - kallisto cite -about: - home: http://pachterlab.github.io/kallisto - license: BSD_2_Clause - summary: Quantifying abundances of transcripts from RNA-Seq data, or more generally - of target sequences using high-throughput sequencing reads. -extra: - copy_test_source_files: true - final: true - identifiers: - - biotools:kallisto - - doi:10.1038/nbt.3519 - skip-lints: - - missing_tests diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml.template b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml.template deleted file mode 100644 index 251f2bf4584085b47df57b0c3415099b3e405133..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml.template +++ /dev/null @@ -1,42 +0,0 @@ -{% set version = "0.48.0" %} - -package: - name: kallisto - version: {{ version }} - -source: - url: https://github.com/pachterlab/kallisto/archive/v{{ version }}.tar.gz - sha256: 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 - -build: - number: 1 - -requirements: - build: - - make - - cmake - - {{ compiler('cxx') }} - - autoconf - - automake - host: - - hdf5 - - zlib - run: - - hdf5 - - zlib - -test: - commands: - - kallisto cite - -about: - home: "http://pachterlab.github.io/kallisto" - license: BSD_2_Clause - summary: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. - -extra: - identifiers: - - biotools:kallisto - - doi:10.1038/nbt.3519 - skip-lints: - - missing_tests diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/common.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/common.sh deleted file mode 100644 index a39329115d4317f0e9848d034adfc1ce9c97bb48..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/common.sh +++ /dev/null @@ -1,99 +0,0 @@ -function is_expected_architecture() { - if [ $(uname -m) != "$1" ]; then - echo -e "\033[1;31;1mThe current script only supports execution on $1 architecture.\033[0m" - return 1 - fi -} - -function set_script_dir() { - local REL_SCRIPT_DIR - REL_SCRIPT_DIR="$(dirname "${BASH_SOURCE[0]}")" || return 1 - SCRIPT_DIR="$(cd "${REL_SCRIPT_DIR}" && pwd)" || return 1 -} - -function delete_a_directory_or_file() { - if [ -e "$1" ]; then - rm -rf "$1" || return 1 - fi -} - -function safely_create_a_directory() { - delete_a_directory_or_file "$1" - mkdir "$1" || return 1 -} - -function conda_initialize() { - __conda_setup="$("$1/bin/conda" 'shell.bash' 'hook' 2>/dev/null)" - if [ $? -eq 0 ]; then - eval "$__conda_setup" - else - if [ -f "$1/etc/profile.d/conda.sh" ]; then - . "$1/etc/profile.d/conda.sh" - else - export PATH="$1/bin:$PATH" - fi - fi - unset __conda_setup -} - -function create_and_activate_conda_env() { - conda deactivate || return 1 - conda env remove -n kallisto -y || return 1 - conda create -n kallisto -c "$1" kallisto=0.48.0 -y || return 1 - conda activate kallisto || return 1 -} - -function generate_execution_result_data() { - EXPECTED_DIR="${SCRIPT_DIR}/Expected" - safely_create_a_directory "$1" || return 1 - kallisto >"$1/kallistoUsage" - - kallisto index -i "$1/transcripts.idx" "$2/transcripts.fasta.gz" - - kallisto quant -i "$1/transcripts.idx" -o "$1/outputQuantification" \ - -b 100 "$2/reads_1.fastq.gz" "$2/reads_2.fastq.gz" - - kallisto quant -i "$1/transcripts.idx" -o "$1/outputSingleEndReads" \ - -b 100 --single -l 180 -s 20 "$2/reads_1.fastq.gz" - - kallisto quant -i "$1/transcripts.idx" -b 30 -o "$1/outputGenomebam" \ - --genomebam --gtf "$2/transcripts.gtf.gz" --chromosomes \ - "$2/chrom.txt" "$2/reads_1.fastq.gz" "$2/reads_2.fastq.gz" -} - -function generate_HDF5_intermediate_alignment_files() { - for i in "$@"; do - for j in "$i/outputGenomebam" "$i/outputQuantification" "$i/outputSingleEndReads"; do - if [ ! -e "$j" ]; then - echo -e "\033[1;31;1mThe current path does not exist. [$j]\033[0m" - return 1 - fi - delete_a_directory_or_file "$j/abundance.h5.ali" - # To use h5dump, kallisto needs to be installed in the conda environment. - h5dump "$j/abundance.h5" >"$j/abundance.h5.ali" - if [ $? -eq 1 ]; then - echo -e "\033[1;31;1mh5dump execution failed,Please rerun the current script.\033[0m" - return 1 - fi - done - done -} - -function print_execution_result() { - if [ "$1" -eq 0 ]; then - echo -e "\033[1;32;1m'$2' executed successfully.\n\033[0m" - else - echo -e "\033[1;31;1m'$2' execution result does not match expected result.\n\033[0m" - return "$1" - fi -} - -function compare_file_content_by_diff() { - diff "$1" "$2" >/dev/null - print_execution_result "$?" "$3" || return 1 -} - -function compare_file_content_by_cmp() { - cmp "$1" "$2" >/dev/null - print_execution_result "$?" "$3" || return 1 -} diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh deleted file mode 100644 index 217e829f66c0ec0b64288439f4c9ebfa155c028b..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh +++ /dev/null @@ -1,50 +0,0 @@ -#!/bin/bash - -source "$( - cd "$(dirname "$0")" || exit 1 - pwd -)/common.sh" - -function download_test_case_data() { - TEST_CASE_DIR="${SCRIPT_DIR}/TestCase" - safely_create_a_directory "${TEST_CASE_DIR}" || return 1 - wget -c -O "${TEST_CASE_DIR}/kallisto-0.48.0.tar.gz" https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - if [ $? -eq 1 ]; then - echo -e "\033[1;31;1mTest case download failed,Please rerun the current script.\033[0m" - return 1 - fi - tar -C "${TEST_CASE_DIR}" \ - -xzf "${TEST_CASE_DIR}/kallisto-0.48.0.tar.gz" \ - kallisto-0.48.0/test/reads_1.fastq.gz \ - kallisto-0.48.0/test/reads_2.fastq.gz \ - kallisto-0.48.0/test/transcripts.fasta.gz \ - kallisto-0.48.0/test/transcripts.gtf.gz \ - kallisto-0.48.0/test/chrom.txt \ - --strip-components 2 --no-same-owner - if [ $? -eq 1 ]; then - echo -e "\033[1;31;1mExtraction failed.\033[0m" - return 1 - fi - rm -rf "${TEST_CASE_DIR}/kallisto-0.48.0.tar.gz" || return 1 -} - -function main() { - is_expected_architecture x86_64 || return 1 - set_script_dir || return 1 - download_test_case_data || return 1 - conda_initialize "$1" - create_and_activate_conda_env bioconda || return 1 - local EXPECTED_DIR - EXPECTED_DIR="${SCRIPT_DIR}/Expected" - generate_execution_result_data "${EXPECTED_DIR}" "${TEST_CASE_DIR}" - if [[ $? -eq 0 ]]; then - echo -e "\033[1;32;1mSuccessfully generated expected data.\033[0m" - else - echo -e "\033[1;31;1mFailed to generate expected data.\033[0m" - delete_a_directory_or_file "${TEST_CASE_DIR}" - delete_a_directory_or_file "${EXPECTED_DIR}" - fi -} - -# /bin/bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh /root/anaconda3 -main "$@" diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh deleted file mode 100644 index 28bf8a6328bfc188df60cd595168da13c2803916..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -source "$( - cd "$(dirname "$0")" || exit 1 - pwd -)/common.sh" - -function main() { - is_expected_architecture aarch64 || return 1 - set_script_dir || return 1 - conda_initialize "$1" - create_and_activate_conda_env local || return 1 - local TEST_CASE_DIR - TEST_CASE_DIR="${SCRIPT_DIR}/TestCase" - local PRACTICAL_DIR - PRACTICAL_DIR="${SCRIPT_DIR}/Practical" - generate_execution_result_data "${PRACTICAL_DIR}" "${TEST_CASE_DIR}" - if [[ $? -eq 0 ]]; then - echo -e "\033[1;32;1mSuccessfully generated practical data.\033[0m" - else - echo -e "\033[1;31;1mFailed to generate practical data.\033[0m" - delete_a_directory_or_file "${TEST_CASE_DIR}" - delete_a_directory_or_file "${PRACTICAL_DIR}" - fi -} - -# /bin/bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh /root/anaconda3 -main "$@" diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/run_test.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/run_test.sh deleted file mode 100755 index a4f17f4a5818157989872f3ca53d7fe3cdb5fdb0..0000000000000000000000000000000000000000 --- a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/run_test.sh +++ /dev/null @@ -1,68 +0,0 @@ -#!/bin/bash - -source "$( - cd "$(dirname "$0")" || exit 1 - pwd -)/common.sh" - -function set_dir() { - EXPECTED_DIR="${SCRIPT_DIR}/Expected" || return 1 - PRACTICAL_DIR="${SCRIPT_DIR}/Practical" || return 1 - TEST_CASE_DIR="${SCRIPT_DIR}/TestCase" || return 1 -} - -function comparison_of_quantification_results() { - # The ignored fields "start_time" and "call" are related to the command execution time stop and parameter path, not due to feature comparison - diff <(sed '11,12d' "$1/run_info.json") <(sed '11,12d' "$2/run_info.json") >/dev/null || return 1 - # Mainly ignore the difference between the generated HDF5 file path, the absolute path of the executed command and the time stamp. - diff <(sed '1d;428d;435d;570d;571d' "$1/abundance.h5.ali") <(sed '1d;428d;435d;570d;571d' "$2/abundance.h5.ali") >/dev/null || return 1 - diff "$1/abundance.tsv" "$2/abundance.tsv" >/dev/null || return 1 -} - -function visualize_the_pseudoalignments_comparison_of_results() { - comparison_of_quantification_results "$1" "$2" || return 1 - cmp "$1/pseudoalignments.bam" "$2/pseudoalignments.bam" >/dev/null || return 1 - cmp "$1/pseudoalignments.bam.bai" "$2/pseudoalignments.bam.bai" >/dev/null || return 1 -} - -function start_test() { - compare_file_content_by_diff "$1/kallistoUsage" "$2/kallistoUsage" \ - "kallisto" || return 1 - - compare_file_content_by_cmp "$1/transcripts.idx" "$2/transcripts.idx" \ - "kallisto index -i transcripts.idx transcripts.fasta.gz" || return 1 - - comparison_of_quantification_results "$1/outputQuantification" "$2/outputQuantification" - print_execution_result "$?" "kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz" || return 1 - - comparison_of_quantification_results "$1/outputSingleEndReads" "$2/outputSingleEndReads" - print_execution_result "$?" "kallisto quant -i transcripts.idx -o output -b 100 --single -l 180 -s 20 reads_1.fastq.gz" || return 1 - - visualize_the_pseudoalignments_comparison_of_results "$1/outputGenomebam" "$2/outputGenomebam" - print_execution_result "$?" "kallisto quant -i transcripts.kidx -b 30 -o kallisto_out --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt reads_1.fastq.gz reads_2.fastq.gz" || return 1 -} - -function test_clean() { - for i in "$@"; do - delete_a_directory_or_file "$i" - done -} - -function main() { - is_expected_architecture aarch64 || return 1 - set_script_dir || return 1 - set_dir || return 1 - conda_initialize "$1" - create_and_activate_conda_env local || return 1 - generate_HDF5_intermediate_alignment_files "${EXPECTED_DIR}" "${PRACTICAL_DIR}" || return 1 - start_test "${EXPECTED_DIR}" "${PRACTICAL_DIR}" - if [[ $? -eq 0 ]]; then - echo -e "\033[1;32;5mThe test was successful.\n\033[0m" - else - echo -e "\033[1;31;1mTest failed.\n\033[0m" - fi - test_clean "${TEST_CASE_DIR}" "${EXPECTED_DIR}" "${PRACTICAL_DIR}" || return 1 -} - -# /bin/bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh /root/anaconda3 -main "$@" diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 0fbae3f8c71f4f843628c6f1469a0b5e2d7ead3a..0b69981b775d1ea28f0309340b25972be3f1fb51 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -6,4 +6,5 @@ Life Sciences Software List: - repositories: RepeatMasker-4.1.2 - repositories: eigensoft-7.2.1 - repositories: redundans-v0.13c -- repositories: bamtools-2.5.2 \ No newline at end of file +- repositories: bamtools-2.5.2 +- repositories: falcon-v0.3.0 \ No newline at end of file diff --git a/LifeSciences/eigensoft-7.2.1/dependency/Anaconda3.sh b/LifeSciences/eigensoft-7.2.1/dependency/Anaconda3.sh new file mode 100644 index 0000000000000000000000000000000000000000..4cfa939663e43eca8c603634aefa49ec6042123a --- /dev/null +++ b/LifeSciences/eigensoft-7.2.1/dependency/Anaconda3.sh @@ -0,0 +1,50 @@ +#!/bin/bash + + +### 使用Anaconda3来安装python依赖 +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./miniconda-py38_4.11.0-devel.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi + +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi +[[ "$buildpath" == "$installpath" ]] && echo "构建路径与安装路径需为不同路径" && exit 1 +yum install -y wget tar cmake environment-modules --nogpgcheck +wget -t 0 -c -P $buildpath https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-aarch64.sh + +sh $buildpath/Anaconda3-2021.04-Linux-aarch64.sh -b -p $installpath/Anaconda3 + +$installpath/Anaconda3/bin/conda conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ +$installpath/Anaconda3/bin/conda conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ +$installpath/Anaconda3/bin/conda conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge +$installpath/Anaconda3/bin/conda conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/ + +$installpath/Anaconda3/bin/conda create --name python27 python=2.7 + +source activate python27 + +cat>"$installpath/Anaconda3/anaconda3_modulefiles"<"$installpath/nim-0.18.0/nim_modulefiles"<"pkg/falcon-v0.3.0-hpc/run.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! \$d =~ "FALCON-master" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done + +module use \$current_dir/FALCON-master/FALCON-integrate/fc_env/ +moudle load \$current_dir/FALCON-master/FALCON-integrate/fc_env/falcon_modulefiles + +cd \$current_dir +EOF +cd pkg/ && tar zcvf falcon-v0.3.0-hpc.tar.gz falcon-v0.3.0-hpc + +rm -rf $buildpath $installpath diff --git a/LifeSciences/falcon-v0.3.0/dependency/Anaconda3.sh b/LifeSciences/falcon-v0.3.0/dependency/Anaconda3.sh new file mode 100644 index 0000000000000000000000000000000000000000..703be53db9927f39156e3836f0cbd80b329f9e92 --- /dev/null +++ b/LifeSciences/falcon-v0.3.0/dependency/Anaconda3.sh @@ -0,0 +1,52 @@ +#!/bin/bash + + +### 使用Anaconda3来安装python依赖 +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./miniconda-py38_4.11.0-devel.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi + +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi +[[ "$buildpath" == "$installpath" ]] && echo "构建路径与安装路径需为不同路径" && exit 1 +yum install -y wget tar cmake environment-modules --nogpgcheck +wget -t 0 -c -P $buildpath https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-aarch64.sh + +bash $buildpath/Anaconda3-2021.11-Linux-aarch64.sh -b -p $installpath/Anaconda3 + +$installpath/Anaconda3/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ +$installpath/Anaconda3/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ +$installpath/Anaconda3/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge +$installpath/Anaconda3/bin/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/ + +echo "y" > input.data +$installpath/Anaconda3/bin/conda create --name python27 python=2.7 < input.data +rm -rf input.data +source activate python27 + +cat>"$installpath/Anaconda3/anaconda3_modulefiles"<"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles"<"$installpath/nim-0.18.0/nim_modulefiles"<"$installpath/FALCON-master/FALCON-integrate/fc_env/falcon_modulefiles"<