bwawrik/bioinformatics repository overview

⁠centos 7

⁠:LATEST

--dependencies --

'Develpment Tools'; wget; nano; sudo; zlib-devel.x86_64; gsl-devel.x86_64; libpng.x86_64; libpng12.x86_64; python-devel.x86_64; java-devel; ncurses-devel; ncurses; gnuplot.x86_64; R; PIP; perl-CPAN; perl-Time-HiRes; perl-local-lib.noarch; python-pip.noarch; ruby-devel.x86_64; perl-Module-Build; perl-Bit-Vector; perl-SVG; perl-DBI; perl-XML-Parser
perl-Carp-Clan; perl-Class-Inspector; perl-HTML-Parser; perl-SOAP-Lite
perl-URI; perl-Inline; perl-Parse-RecDescent; perl-version; perl-DBD-MySQL; ruby gems: gnuplot, narray, RubyInline, terminal-table; perl-JSON::XS; perl-SVG; perl-Bit::Vector; Cython.x86_64; scipy.x86_64; numpy.x86_64; openmpi.x86_64; openmpi-devel.x86_64; mpich2.x86_64; mpich-devel.x86_64; mpich.x86_64

-- bioinformatics software --

Bioperl | http://www.bioperl.org/wiki/Main_Page⁠ Biopieces https://code.google.com/p/biopieces/⁠ Biopython | http://biopython.org/wiki/Main_Page⁠ BLAST suite | http://blast.ncbi.nlm.nih.gov⁠ blat | http://www.kentinformatics.com/⁠ bowtie | http://bowtie-bio.sourceforge.net/index.shtml⁠ bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml⁠ bwa | http://bio-bwa.sourceforge.net/⁠ CAP3 | http://seq.cs.iastate.edu/cap3.html⁠ CDBtools | http://sourceforge.net/projects/cdbtools/⁠ cd-hit | http://weizhongli-lab.org/cd-hit/⁠ ChimeraSlayer | http://microbiomeutil.sourceforge.net/⁠ Cutadapt https://code.google.com/p/cutadapt/⁠ CytoScape | http://www.cytoscape.org/⁠ Diamond | http://ab.inf.uni-tuebingen.de/software/diamond/⁠ ea-utils.1.1.2-537 https://code.google.com/p/ea-utils/⁠ EMIRGE https://github.com/csmiller/EMIRGE⁠ FastQC | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/⁠ fastx-toolkit 0.0.12 | http://hannonlab.cshl.edu/fastx_toolkit/⁠ FragGeneScan | http://omics.informatics.indiana.edu/FragGeneScan/⁠ gnuplot | http://www.gnuplot.info/⁠ HMMER 3.0 | http://hmmer.janelia.org/⁠ HomerTools | http://homer.salk.edu/homer/ngs/homerTools.html⁠ - idba https://code.google.com/p/hku-idba/⁠ Jellyfish | http://www.genome.umd.edu/jellyfish.html⁠ MaxBin | http://sourceforge.net/projects/maxbin/⁠ MEGAN 4 | http://ab.inf.uni-tuebingen.de/software/megan5/⁠ mummer | http://mummer.sourceforge.net/⁠ Muscle | http://www.ebi.ac.uk/Tools/msa/muscle/⁠ Prodigal | http://prodigal.ornl.gov/⁠ Pysam https://pypi.python.org/packages/source/p/pysam/⁠ Ray 2.2.0 | http://denovoassembler.sourceforge.net/⁠ RDP Classifier | http://downloads.sourceforge.net/project/rdp-classifier⁠ Samtools | http://samtools.sourceforge.net/⁠ SeqPrep https://github.com/jstjohn/SeqPrep⁠ SMALT https://www.sanger.ac.uk/resources/software/smalt/⁠ SourceTracker | http://downloads.sourceforge.net/project/sourcetracker⁠ Trimmomatic | http://www.usadellab.org/cms/?page=trimmomatic⁠ Velvet https://www.ebi.ac.uk/~zerbino/velvet/⁠ vserach https://github.com/torognes/vsearch⁠ RAPSearch2.23 | http://sourceforge.net/projects/rapsearch2/⁠ Qiime | http://qiime.org⁠

⁠============================================================ :ASSEMBLY

--dependencies --

'Develpment Tools'; wget; nano; sudo; zlib-devel.x86_64; openmpi.x86_64; openmpi-devel.x86_64; mpich2.x86_64; mpich-devel.x86_64; mpich.x86_64

-- bioinformatics software --

zlib-devel.x86_64; Prodigal 2.50; FragGeneScan1.19; Velvet 1.2.10; cap3; Ray 2.3.2

⁠============================================================ :V_03

--dependencies --

'Develpment Tools'; wget; nano; sudo; zlib-devel.x86_64; gsl-devel.x86_64; libpng.x86_64; libpng12.x86_64; python-devel.x86_64; java-devel; ncurses-devel; ncurses; gnuplot.x86_64; R; PIP; perl-CPAN; perl-Time-HiRes; perl-local-lib.noarch; python-pip.noarch; ruby-devel.x86_64; perl-Module-Build; perl-Bit-Vector; perl-SVG; perl-DBI; perl-XML-Parser
perl-Carp-Clan; perl-Class-Inspector; perl-HTML-Parser; perl-SOAP-Lite
perl-URI; perl-Inline; perl-Parse-RecDescent; perl-version; perl-DBD-MySQL; ruby gems: gnuplot, narray, RubyInline, terminal-table; perl-JSON::XS; perl-SVG; perl-Bit::Vector

-- bioinformatics software --

ea-utils.1.1.2-537; blat; cutadapt 1.3; fastQC; blast 2.2.30+; BWA; bowtie; bowtie2; muscle 3.8.31; idba; Prodigal 2.50; FragGeneScan 1.19; Velvet 1.2.10; Samtools 1.2; MUMmer3.23; smalt-0.7.5; cap3; jellyfish-2.2.0; HMMer-3.1b1; MEGAN5; MaxBin-1.4.2; cdbtools; cd-hit; RDP Classifier; sourcetracker; vsearch; fastx_toolkit_0.0.13; HomerTools; R(SeqLogo); Trimmomatic-0.32; biopython; biopieces; microbiomeutil-r20110519 (ChimeraSlayer; NAST-iEr; TreeChopper; WigeroN; AmosCmp16Spipeline)

⁠============================================================ :V_02

--dependencies --

'Develpment Tools'; wget; nano; sudo; zlib-devel.x86_64; gsl-devel.x86_64; libpng.x86_64; libpng12.x86_64; python-devel.x86_64; java-devel; ncurses-devel; ncurses; gnuplot.x86_64; R; PIP; perl-CPAN; perl-Time-HiRes; perl-local-lib.noarch; python-pip.noarch; ruby-devel.x86_64; perl-Module-Build; perl-Bit-Vector; perl-SVG; perl-DBI; perl-XML-Parser
perl-Carp-Clan; perl-Class-Inspector; perl-HTML-Parser; perl-SOAP-Lite
perl-URI; perl-Inline; perl-Parse-RecDescent; perl-version; perl-DBD-MySQL; ruby gems: gnuplot, narray, RubyInline, terminal-table; perl-JSON::XS; perl-SVG; perl-Bit::Vector

-- bioinformatics software --

ea-utils.1.1.2-537; blat; cutadapt 1.3; fastQC; blast 2.2.30+; BWA; bowtie; bowtie2; muscle 3.8.31; idba; Prodigal 2.50; FragGeneScan 1.19; Velvet 1.2.10; Samtools 1.2; MUMmer3.23; smalt-0.7.5; cap3; jellyfish-2.2.0; HMMer-3.1b1; MEGAN5; MaxBin-1.4.2; cdbtools; cd-hit; RDP Classifier; sourcetracker; vsearch; fastx_toolkit_0.0.13; HomerTools; R(SeqLogo); Trimmomatic-0.32; biopython; biopieces

⁠============================================================ :V_01

--dependencies --

'Develpment Tools'; wget; nano; sudo; zlib-devel.x86_64; gsl-devel.x86_64; libpng.x86_64; libpng12.x86_64; python-devel.x86_64; java-devel; ncurses-devel; ncurses; gnuplot.x86_64; R;

-- bioinformatics software --

ea-utils.1.1.2-537; blat; cutadapt 1.3; fastQC; blast 2.2.30+; BWA; bowtie; bowtie2; muscle 3.8.31; idba; Prodigal 2.50; FragGeneScan 1.19; Velvet 1.2.10; Samtools 1.2; MUMmer3.23; smalt-0.7.5; cap3; jellyfish-2.2.0; HMMer-3.1b1; MEGAN5; MaxBin-1.4.2; cdbtools; cd-hit; RDP Classifier; sourcetracker; vsearch; fastx_toolkit_0.0.13; ;