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 new file mode 100644 index 0000000000000000000000000000000000000000..d58e060f266a128e9c65a46e7bf58ed839752fa9 --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/cloudbuild/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +conda build $(dirname $(dirname "$0"))/recipe 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 new file mode 100644 index 0000000000000000000000000000000000000000..7a9bdfb1e572259daf13d941bdd3169b67e72546 Binary files /dev/null and b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/conda-bld/kallisto-0.48.0-h0d531b0_1_kp.tar.bz2 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 new file mode 100644 index 0000000000000000000000000000000000000000..f3cd874d4aceb5b6d0c592be3dd0df770f4addeb --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/dependencies/DependencyList @@ -0,0 +1 @@ +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\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" new file mode 100644 index 0000000000000000000000000000000000000000..afeee6711b2ad7224e443e5b2386b3b661425605 --- /dev/null +++ "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" @@ -0,0 +1,452 @@ +# 在 Linux 环境下将 conda x86 架构的软件包迁移至 aarch64 架构的软件包 + +> 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" new file mode 100644 index 0000000000000000000000000000000000000000..afe947e22914985ff2cc273a3c3e07eee13b44e5 --- /dev/null +++ "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" @@ -0,0 +1,187 @@ +# 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 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b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/documentation/images/image-guide-016.png 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 new file mode 100644 index 0000000000000000000000000000000000000000..6c2dd25276e96a04432f791c4eb210e4471440a8 --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/build.sh @@ -0,0 +1,15 @@ +#!/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 new file mode 100644 index 0000000000000000000000000000000000000000..4c754a45dcc1b0b9ccde417785938d5de41e634f --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/conda_build_config.yaml 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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 new file mode 100644 index 0000000000000000000000000000000000000000..24bc1d936e5d6be73393942f057bb06913da8ebf --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml @@ -0,0 +1,104 @@ +# 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 new file mode 100644 index 0000000000000000000000000000000000000000..251f2bf4584085b47df57b0c3415099b3e405133 --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/recipe/meta.yaml.template @@ -0,0 +1,42 @@ +{% 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 new file mode 100644 index 0000000000000000000000000000000000000000..b53a40b54a5f599e52c7a8d93c4dc1dd86f5822f --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/common.sh @@ -0,0 +1,62 @@ +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() { + if [ -e "$1" ]; then + rm -rf "$1" || return 1 + fi +} + +function safely_create_a_directory() { + delete_a_directory "$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" "$2/reads_2.fastq.gz" +} diff --git a/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh new file mode 100644 index 0000000000000000000000000000000000000000..c6f34bb214a1490285435a61b16fcc8d289860d9 --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh @@ -0,0 +1,50 @@ +#!/bin/bash + +source "$( + 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 [[ $? -eq 0 ]]; then + echo -e "\033[1;32;1mSuccessfully generated expected data.\033[0m" + else + echo -e "\033[1;31;1mFailed to generate expected data.\033[0m" + delete_a_directory "${TEST_CASE_DIR}" + delete_a_directory "${EXPECTED_DIR}" + fi +} + +# /bin/bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_expected_data.sh /opt/anaconda3 +main "$@" 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 new file mode 100644 index 0000000000000000000000000000000000000000..e5a14a662e6081d945dd41ef94c88dafd4eb7584 --- /dev/null +++ b/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh @@ -0,0 +1,28 @@ +#!/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 [[ $? -eq 0 ]]; then + echo -e "\033[1;32;1mSuccessfully generated practical data.\033[0m" + else + echo -e "\033[1;31;1mFailed to generate practical data.\033[0m" + delete_a_directory "${TEST_CASE_DIR}" + delete_a_directory "${PRACTICAL_DIR}" + fi +} + +# /bin/bash ~/hpc/Anaconda/bioconda/kallisto/0.48.0/h0d531b0_1/test/generate_practical_data.sh /opt/anaconda3 +main "$@"