fanyucai1/snv repository overview

strace enscript curl wget swig bzip2 ghostscript autoconf automake cmake Cython
    glibc-devel zlib-devel python-devel libcurl libpng libcurl-devel bzip2-devel
    libtool-ltdl libtool-ltdl-devel libxml2-devel pigz ncurses-devel libffi-devel libxslt-devel sqlite-devel tbb-devel audit audit-libs audit-libs-devel
    gcc-gfortran libicu-devel make openblas-devel pango pcre2-devel tcl tk unzip which zip
    perl-CPAN perl-IPC-Cmd perl-WWW-Curl java-11-openjdk java-11-openjdk-devel gcc gcc-c++ glibc-headers
    python2-pip openssl-devel htslib

/software/Python-v3.11.0/bin/python3

/usr/local/bin/R

/software/openlogic-openjdk-jre-17.0.9+9-linux-x64/bin/java

/software/openlogic-openjdk-jre-8u392-b08-linux-x64/bin/java

/software/bwa-0.7.17/bwa
/software/samtools-v1.18/bin/samtools
/software/bcftools-v1.18/bin/bcftools
/software/seqtk-1.4/seqtk
sh -c "export LD_LIBRARY_PATH=/software/htslib-v1.18/lib:$LD_LIBRARY_PATH && /software/pindel-0.2.5b8/pindel"
sh -c "export PATH=/software/gcc-v7.1.0/bin:$PATH && export LD_LIBRARY_PATH=//software/gcc-v7.1.0/lib64/:$LD_LIBRARY_PATH && /software/MuSE-2.0.4/MuSE"
/software/bedtools2/bin/bedtools
/software/strelka-v2.9.10/bin/configureStrelkaGermlineWorkflow.py
/software/strelka-v2.9.10/bin/configureStrelkaSomaticWorkflow.py
/software/manta-v1.6.0/bin/configManta.py
/software/somatic-sniper-1.0.5.0/build/bin/bam-somaticsniper
/software/VarDict-1.8.3/bin/VarDict
/software/minimap2-2.26_x64-linux/minimap2
/software/rtg-tools-3.12.1/rtg
/software/bedops/bin/bedops
/software/gatk-4.4.0.0/gatk
/usr/bin/fastp
/usr/bin/msisensor-pro
/usr/bin/sambamba-1.0.1-linux-amd64-static
/usr/bin/delly_v1.1.8_linux_x86_64bit
/software/openlogic-openjdk-jre-17.0.9+9-linux-x64/bin/java -jar /usr/bin/picard.jar
/software/openlogic-openjdk-jre-17.0.9+9-linux-x64/bin/java -jar /usr/bin/abra2-2.24.jar
/software/openlogic-openjdk-jre-17.0.9+9-linux-x64/bin/java -jar /usr/bin/fgbio-2.1.0.jar