diff --git a/templates/interproscan/5.73-104.0/interproscan.arm.py39.config b/templates/interproscan/5.73-104.0/interproscan.arm.py39.config new file mode 100644 index 0000000000000000000000000000000000000000..f01fd319aa250cb3500e0d4b130d4d89f62a6656 --- /dev/null +++ b/templates/interproscan/5.73-104.0/interproscan.arm.py39.config @@ -0,0 +1,65 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +interproscan/5.53-87.0 http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.73-104.0/interproscan-5.73-104.0-64-bit.tar.gz +bisheng-jdk/11.0.25 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_jdk/bisheng-jdk-11.0.25-linux-aarch64.tar.gz bisheng-jdk-11-aarch64.tar.gz +bisheng-jre/11.0.25 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_jdk/bisheng-jre-11.0.25-linux-aarch64.tar.gz bisheng-jre-11-aarch64.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install python3/3.9.9 bisheng +module load python3/3.9.9 +tar -zxvf ${JARVIS_DOWNLOAD}/bisheng-jdk-11-aarch64.tar.gz -C ${JARVIS_COMPILER} +tar -zxvf ${JARVIS_DOWNLOAD}/bisheng-jre-11-aarch64.tar.gz -C ${JARVIS_COMPILER}/bisheng-jdk-11.0.25/ --transform='s/bisheng-jre-11.0.25/jre/' +echo -e "\033[0;32mCheck the execution dependency \"hmmer\" ...\033[0m" +file1="${JARVIS_ROOT}/hmmer/bin/hmmscan" +file2="${JARVIS_ROOT}/hmmer/bin/hmmsearch" +if [[ $( file -b --mime-encoding ${file1} ) = "binary" ]];then + if [[ $( file -b --mime-encoding ${file2} ) = "binary" ]];then + echo -e "\033[0;32mAlready installed the execution dependency \"hmmer\"\033[0m" + fi +else + echo -e "\033[0;31mPlease install the execution dependency \"hmmer\" in ${JARVIS_ROOT} or configuer the hmmer executabla file environment variables after installation.\033[0m" + exit 1 +fi + +mkdir -p ${JARVIS_ROOT}/software/apps +tar -zxvf ${JARVIS_DOWNLOAD}/interproscan-5.73-104.0-64-bit.tar.gz -C ${JARVIS_ROOT}/software/apps/ --transform='s/interproscan-5.73-104.0/interproscan/' + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load python3/3.9.9 +export PATH=${JARVIS_COMPILER}/bisheng-jdk-11.0.25/bin:${JARVIS_COMPILER}/bisheng-jdk-11.0.25/jre/bin:$PATH + +[APP] +app_name = interproscan +build_dir = ${JARVIS_ROOT}/software/apps/interproscan +binary_dir = ${JARVIS_ROOT}/software/apps/interproscan +case_dir = ${JARVIS_ROOT}/software/apps/interproscan + +[BUILD] +yes | cp -ar ${JARVIS_ROOT}/hmmer/bin/* bin/hmmer/hmmer3/3.3/ +python3 setup.py -f interproscan.properties + +echo -e "\033[0;32mExample: Testing the \"sfld\" module\033[0m" +file -b bin/sfld/sfld_postprocess | grep -qi 'ARM\|aarch64' +if [ $? -eq 0 ];then + echo -e "\033[0;32mAlready \"sfld\" module aarch64 platform binary\033[0m" + echo -e "\033[0;32mNext command ./jarvis -r\033[0m" +else + echo -e "\033[0;31mTo be compiled and replaced with \"bin/sfld/sfld_postprocess\" binaries for aarch64 platforms!\033[0m" + exit 1 +fi + +[CLEAN] + +[RUN] +run = bash interproscan.sh -i +binary = test_all_appl.fasta -f tsv -dp -appl sfld +nodes = 1