# Bioinformatics Applications ## Introduction In addition to the many applications available through modules (deployed through EasyBuild packaging system) we provide an alternative source of applications on our clusters inferred from [Gentoo Linux](https://www.gentoo.org/). The user's environment is setup through a script which returns a bash instance to the user (you can think of it a starting a whole virtual machine but inside your current namespace) . The applications were optimized by gcc compiler for the SandyBridge and IvyBridge platforms. The binaries use paths from /apps/gentoo prefix to find the required runtime dependencies, config files, etc. The Gentoo Linux is a standalone installation not even relying on the glibc provided by host operating system (Redhat). The trick which allowed us to install Gentoo Linux on the host Redhat system is called Gentoo::RAP and uses a modified loader with a hardcoded path ([links](https://wiki.gentoo.org/wiki/Prefix/libc)). ## Starting the Environment ```console mmokrejs@login2~$ /apps/gentoo/startprefix ``` ## Starting PBS Jobs Using the Applications Create a template file which can be used and an argument to qsub command. Notably, the 'PBS -S' line specifies full PATH to the Bourne shell of the Gentoo Linux environment. ```console mmokrejs@login2~$ cat myjob.pbs #PBS -S /apps/gentoo/bin/sh #PBS -l nodes=1:ppn=16,walltime=12:00:00 #PBS -q qfree #PBS -M my_email@foo.bar #PBS -m ea #PBS -N sample22 #PBS -A DD-13-5 #source ~/.bashrc cd $PBS_O_WORKDIR || exit 255 myscript.sh foo 1>myjob.log 2>&1 $ head -n 1 myscript.sh #! /apps/gentoo/bin/sh $ qsub myjob.pbs $ qstat ``` ## Reading Manual Pages for Installed Applications ```console mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man bwa mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man samtools ``` ## Listing of Bioinformatics Applications ```console mmokrejs@login2~$ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt sci-biology/ANGLE-bin-20080813-r1 sci-biology/AlignGraph-9999 sci-biology/Atlas-Link-0.01-r1 sci-biology/BRANCH-9999 sci-biology/EBARDenovo-1.2.2 sci-biology/FLASH-1.2.9 sci-biology/GAL-0.2.2 sci-biology/Gambit-0.4.145 sci-biology/HTSeq-0.6.1 sci-biology/InterMine-0.98 sci-biology/MochiView-1.45 sci-biology/MuSeqBox-5.4 sci-biology/ONTO-PERL-1.41 sci-biology/ORFcor-20130507 sci-biology/Rcorrector-9999 sci-biology/SSAKE-3.8.2 sci-biology/STAR-9999 sci-biology/YASRA-2.33 sci-biology/abacas-1.3.1 sci-biology/align_to_scf-1.06 sci-biology/assembly-stats-9999 sci-biology/bambus-2.33 sci-biology/bamtools-9999 sci-biology/bcftools-1.2 sci-biology/bedtools-2.22.1 sci-biology/bfast-0.7.0a sci-biology/biobambam2-9999 sci-biology/bismark-0.13.0 sci-biology/blat-34-r1 sci-biology/blue-1.1.3 sci-biology/bowtie-2.2.9 sci-biology/brat-1.2.4 sci-biology/bwa-0.7.13 sci-biology/bx-python-9999 sci-biology/cast-bin-20080813 sci-biology/cd-hit-4.6.5 sci-biology/cdbfasta-0.1 sci-biology/clover-2011.10.24 sci-biology/clustalw-2.1 sci-biology/cnrun-2.0.3 sci-biology/codonw-1.4.4-r2 sci-biology/conform-gt-1174 sci-biology/conifer-0.2.2 sci-biology/coral-1.4 sci-biology/cross_genome-20140822 sci-biology/cutadapt-9999 sci-biology/dawg-1.1.2 sci-biology/dna2pep-1.1 sci-biology/edena-3.131028 sci-biology/epga-9999 sci-biology/erpin-5.5b sci-biology/estscan-3.0.3 sci-biology/eugene-4.1d sci-biology/exonerate-gff3-9999 sci-biology/fastx_toolkit-0.0.14 sci-biology/gemini-9999 sci-biology/geneid-1.4.4 sci-biology/genepop-4.2.1 sci-biology/glimmerhmm-3.0.1-r1 sci-biology/gmap-2015.12.31.5 sci-biology/hexamer-19990330 sci-biology/hts-python-9999 sci-biology/jellyfish-2.1.4 sci-biology/jigsaw-3.2.10 sci-biology/kallisto-9999 sci-biology/karect-1.0.0 sci-biology/lastz-1.03.66 sci-biology/libgtextutils-0.6.1 sci-biology/lucy-1.20 sci-biology/megahit-9999 sci-biology/merlin-1.1.2 sci-biology/miranda-3.3a sci-biology/mreps-2.5 sci-biology/mrfast-2.6.0.1 sci-biology/mummer-3.22-r1 sci-biology/muscle-3.8.31 sci-biology/nrcl-110625 sci-biology/nwalign-0.3.1 sci-biology/oases-9999 sci-biology/parafly-20130121 sci-biology/phrap-1.080812-r1 sci-biology/phred-071220 sci-biology/phylip-3.696-r1 sci-biology/plinkseq-0.10 sci-biology/primer3-2.3.7 sci-biology/prinseq-lite-0.20.4 sci-biology/proda-1.0 sci-biology/pybedtools-0.6.9 sci-biology/pysam-0.9.0 sci-biology/pysamstats-0.24.2 sci-biology/quast-2.3 sci-biology/quorum-1.0.0 sci-biology/reaper-15348 sci-biology/repeatmasker-libraries-20150807 sci-biology/reptile-1.1 sci-biology/samstat-20130708 sci-biology/samtools-0.1.20-r2 sci-biology/samtools-1.3-r1 sci-biology/scaffold_builder-20131122-r1 sci-biology/scan_for_matches-20121220 sci-biology/screed-0.7.1 sci-biology/scythe-0.992 sci-biology/seqan-2.1.1 sci-biology/seqtools-4.34.5 sci-biology/sff_dump-1.04 sci-biology/sgp2-1.1 sci-biology/shrimp-2.2.3 sci-biology/sickle-9999 sci-biology/smalt-0.7.6 sci-biology/snpomatic-9999 sci-biology/ssaha2-bin-2.5.5 sci-biology/stampy-1.0.28 sci-biology/stringtie-1.2.2 sci-biology/subread-1.4.6 sci-biology/swissknife-1.72 sci-biology/tagdust-20101028 sci-biology/tclust-110625 sci-biology/tigr-foundation-libs-2.0-r1 sci-biology/trans-abyss-1.4.8 sci-biology/trf-4.07b sci-biology/uchime-4.2.40 sci-biology/velvet-1.2.10 sci-biology/velvetk-20120606 sci-biology/zmsort-110625 ``` ```console mmokrejs@login2~$ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt sci-libs/amd-2.3.1 sci-libs/blas-reference-20151113-r1 sci-libs/camd-2.3.1 sci-libs/cbflib-0.9.3.3 sci-libs/ccolamd-2.8.0 sci-libs/cholmod-2.1.2 sci-libs/coinor-cbc-2.8.9 sci-libs/coinor-cgl-0.58.6 sci-libs/coinor-clp-1.15.6-r1 sci-libs/coinor-dylp-1.9.4 sci-libs/coinor-osi-0.106.6 sci-libs/coinor-utils-2.9.11 sci-libs/coinor-vol-1.4.4 sci-libs/colamd-2.8.0 sci-libs/cxsparse-3.1.2 sci-libs/dcmtk-3.6.0 sci-libs/gsl-2.1 sci-libs/hdf5-1.8.15_p1 sci-libs/htslib-1.3 sci-libs/io_lib-1.14.7 sci-libs/lapack-reference-3.6.0-r1 sci-libs/lemon-1.3-r2 sci-libs/libmaus2-9999 sci-libs/qrupdate-1.1.2-r1 sci-libs/scikits-0.1-r1 sci-libs/suitesparseconfig-4.2.1 sci-libs/umfpack-5.6.2 ``` ## Classification of Applications | Applications for bioinformatics at IT4I | | | --------------------------------------- | ------ | | error-correctors | 6 | | aligners | 20 | | clusterers | 5 | | assemblers | 9 | | scaffolders | 6 | | motif searching | 6 | | ORF/gene prediction/genome annotation | 13 | | genotype/haplotype/popullation genetics | 3 | | phylogenetics | 1 | | transcriptome analysis | 2 | | utilities | 15 | | GUI | 3 | | libraries | 4 | | **Total** | **93** |  ## Other Applications Available Through Gentoo Linux Gentoo Linux is a allows compilation of its applications from source code while using compiler and optimize flags set to user's wish. This facilitates creation of optimized binaries for the host platform. Users maybe also use several versions of gcc, python and other tools. ```console mmokrejs@login2~$ gcc-config -l mmokrejs@login2~$ java-config -L mmokrejs@login2~$ eselect ```