LPM: Local Package Manager

Want to install software without root?

Available packages in the standard public repository.

nameverdescriptionnotetested onwebpagedepend on
abyss-mpi1.9.0ABySS assembler (MPI)RHEL 6.4linksparsehash
abyss1.5.1ABySS assembler (Non-MPI)CentOS 6.2link
ack2.12ack: a tool like grep, optimized for programmerslink
allpaths-lg48744ALLPATHS-LG Genome AssemblerCentOS 6.4linkgcc4.7+
amos3.1.0AMOS is a collection of tools and class interfaces for the assembly of DNA reads.SL6.1link
ant1.9.6antCentOS 6.6link
arachne3.2_March9_2009Arachne assemblerSL6.1link
asciiplotsASCII plotCentOS 6.5link
aspera-connect-client3.3.3.81344Aspera Connect Client (commercial; only client is available free of charge; Linux; x86_64)CentOS 6.3link
augustus3.0.2gene prediction program AugustusRHEL 6.1linkboost
autossh1.4cautosshlink
bam2fastq1.1.0The BAM format is an efficient method for storing and sharing data from modern, highly parallel sequencers. While primarily used for storing alignment information, BAMs can (and frequently do) store unaligned reads as well.SL6.1link
bamtoolsBAMtools is a project that provides both a C++ API and a command-line toolkit for reading,SL6.1linkcmake
bedtools2.18.1BEDTools is an extensive suite of utilities for comparing genomic features in BED format.CentOS 6.4link
bfast0.7.0BFAST Blat-like Fast Accurate Search ToolSL6.1link
bioawkBioAwkCentOS 6.4link
biopython1.56BioPythonSL6.1link
biotoolbox1.12.3biotoolboxCentOS 6.4link
blasrBLASR Basic Local Alignment with Successive RefinementCentOS 6.6,RHEL6.1linkhdf5
blast+2.2.31+NCBI BLAST+CentOS 6.4link
blast2.2.26Legacy NCBI BLASTCentOS 6.4link
blat3.5BLATSL6.1link
boost-with-mpi1.49.0Boost library with Boost.MPI (for C++)SL6.1link
boost1.58.0Boost library (for C++)RHEL6.4link
bowtie1.0.0bowtieSL6.1link
bowtie22.2.5bowtie2CentOS 6.6link
bsmap2.5bsmap Bisulfite Sequence Mapping ProgramSL6.1link
bwa-mem0.7.10Burrows-Wheeler Aligner (BWA) Latest version with bwa-mem (still unstable?).CentOS 6.4link
bwa0.6.2Burrows-Wheeler Aligner (BWA) Recommended stable version for sampe.CentOS6.4link
cabog7.0CABOG is scientific software for biological research.SL6.1link
cegmav2.4.010312CEGMA - Core Eukaryotic Genes Mapping ApproachRHEL6.1link
centroidfold0.0.10Centroidfoldlink
chapel1.8.0Chapel: Parallel Programming LanguageRHEL 6.3link
cmake2.8.12.2CMake the cross-platform, open-source build system.SL6.1link
compiler-envs1.3Set environmental variables for compilers.SL6.1link
cpas1.09cpas (CPp As a Script)SL6.1link
cppunit1.12.1CppUnitSL6.3link
ctags5.8Excuberant ctagslink
cufflinks2.2.1Cufflinks Transcript assembly, differential expression, and differential regulation for RNA-SeqSL6.1link
dictd1.11.2dictdSL6.1link
dindel1.01Dindel is a program for calling small indels from short-read sequence dataSL6.1link
dwgsim0.1.10dwgsimCentOS 6.4link
eutils2012Aug08E-utilities for NCBI Entrez DirectCentOS 6.4link
exonerate2.2.0ExonerateCentOS 6.4link
expat2.1.0expat SL6.1link
fastqc0.10.0FastQCSL6.1link
fastx-toolkit0.0.13.2fastx-toolkitSL6.1linklibgtextutils
freeglut2.8.1FreeGLUTlink
gcc4.9.0GCC (latest stable)CentOS 6.5linkgmp mpc mpfr
gcc474.7.3GCC 4.7.3CentOS 6.4linkgmp mpc mpfr
gcc484.8.2GCC 4.8.2CentOS 6.4linkgmp mpc mpfr
geneid1.4.4geneid: a program to predict genes in genomic sequencesRedHat 6.1link
ghc7.8.3GHC The Glasgow Haskell CompilerSL6.1link
git2.4.6gitCent OS 6.4linkautotools
glancesa system monitoring tool (works on curses)linkpython
gmp5.1.2GMP (The GNU Multiple Precision Arithmetic Library)CentOS 6.4link
gnuparallel20140322GNU parallelCentOS 6.4link
gsl1.16GSL GNU Scientific LibraryCentOS 6.4link
gtest1.6.0Google Testlink
haskellplatform2014.2.0.0Haskell PlatformCentOS 6.4linkghc-7.8.3
hdf51.8.15-patch1HDF5 Hierarchical Data FormatCentOS 6.6,RHEL6.1link
hgap1.4HGAP: Hierarchical Genome Assembly ProcessSL6.3link
hitec1.0.2HiTeC high-throughput sequencing data, such as those generated by the Illumina Genome Analyzer. SL6.1link
hmmer33.1b1HMMER - biosequence analysis using profile hidden Markov modelslink
idba-ud1.1.1Iterative De Bruijn graph de novo assembler for short reads with highly Uneven DepthCentOS 6.4link
idba1.1.1Iterative De Bruijn graph AssemblerCentOS 6.4link
igv2.3.14Integrative Genomics ViewerCentOS 6.4link
igvtools2.3.14Integrative Genomics Viewer ToolsCentOS 6.4link
javahome_rhel1.0Set up JAVA_HOME for RedHat Enterprise Linux (or equivalents)RHEL6.4linkjava-1.x.0-openjdk-devel
javalib1.0Set up CLASSPATH for Java librariesSL6.1link
jellyfish1.1.11JELLYFISH - Fast, Parallel k-mer Counting for DNA (Version 1.1.11)CentOS6.4link
jq1.3./jqCentOS 6.4link
klabklab: Kasahara lab. public repository (mostly for various bioinformatics tools)CentOS6.3link
lapack3.4.2LAPAK is a library of Fortran 90 with subroutines for solvingSL6.1link
last418LAST finds similar regions between sequences.CentOS 6.4link
ldc20.14.0LDC - the LLVM-based D compilerUbuntu 12link
lftp4.4.9lftplink
libbz21.0.6bzlib (bzip2)link
libevent2.0.21libeventCentOS 6.4link
libgtextutils0.6libgtextutilslink
libmaa1.2.0libmaalink
lua5.3.1LuaCentOS 6.4link
lua515.1.5Lua 5.1.xCentOS 6.4link
luajit2.0.4LuaJITCentOS 6.4link
macsMACSCentOS6.4link
mafft7.058Multiple alignment program for amino acid or nucleotide sequencesCentOS 6.4link
masurca2.0.3.1MaSuRCA assemblerlink
matplotlib1.4.3matplotlib: a python 2D plotting libraryCentOS 6.4link
maven3.1.1mavenlink
mpc1.0.1MPClink
mpfr3.1.2GNU MPFR LibraryCentOS 6.4link
mpiompio libraryCentOS 6.4link
msgpack-rpc0.3.1Message Pack RPC for C++linkmpio
msgpackMessage Pack for C++link
mummer3.23MUMmer (alignment program using Suffix Tree)CentOS6.4link
muscle3.8.31MUSCLE: Multiple Alignment ProgramCentOS 6.4link
musica22.1.1MuSICA2link
mysql5.6MySQLCentOS 6.1linkcmake
ncbigenome2.7.6NCBI Genome Workbenchlink
netcat0.7.1netcatlink
nextclipNextClip: Clip and analyse Illumina Nextera Long Mate Pair readsCentOS6.6link
ngsutilsNGSUtils: Tools for next-generation sequencing analysisCentOS6.6link
novoalign3.02.02Sensitive sequence aligner (commercial; Linux 2.6; x86_64)CentOS 6.4link
oases0.2.08Oases is a de novo transcriptome assembler designed to SL6.1link
ocaml4.02OCamllink
onlinecall0Online CallSL6.1link
pacbiotoca7.0PacBioToCACentOS 6.3link
pbjelly14.9.9PBJelly: Gap closure tool for PacBio long reads (renamed to pbsuite)link
pbsim1.0.3PBSim: Read simulator for PacBio RSlink
pbsuite14.9.9Analysis tool for PacBio Long ReadsRHEL 6.5link
pbzip21.1.6pbzip2link
pear0.9.6PEAR: Paired-end read mergerCentOS6.6link
peassembler1.2PE-Assemblerlink
pfi-commonpfi-common: General Purpose C++ library for GCC 4.1.2 and laterSL6.1link
picard1.129Picard (SAM manipulation)CentOS 6.6link
pigz2.3pigzCentOS 6.4link
pkgconfig0.28pkg-configSL6.1link
plantuml7986PlantUML link
platanus1.2.1Platanus genome assemblerCentOS 6.6link
porg0.6Porg (Package organizer)link
pv1.5.7Pipe Viewer: a terminal-based tool for monitoring the progress of data through a pipelinelink
pysam0.7.5pysamCentOS 6.4link
python-setuptools0.6c11python setuptoolslinkpython
python2.7.6Python (2.x)link
python33.4.0python3 (3.x)CentOS 6.5link
quast2.3QUAST: Quality Assessment Tool for Genome AssembliesCentOS 6.6linkmatplotlib
R3R language for statistical computing
CentOS 6.5link
recon1.07RECON: a package for automated de novo identification of repeat families from genomic sequenceslink
repeatmaskeropen-4-0-3RepeatMaskerlinkrecon, trf, rmblast
repeatmodeleropen-1-0-7RepeatModeler to prepare species specific database for RepeatMaskerRHEL6.4linkRepeatMasker & Libraries, RECON, RepeatScout, TRF, rmblast
rlwrap0.37rlwrap is a wrapper that uses the GNU readline library to allow the editing of keyboard input for any other command.CentOS6.4linkreadline
rmblastn2.2.28RMBlast - A modified version of NCBI Blast for use with RepeatMasker and RepeatModelerCentOS 6.4link
rsem1.2.18RNA-Seq by Expectation-Maximizationlink
ruby2.2.2Ruby (2.x)link
ruby191.9.3-p545Ruby (1.9.x)link
samtools-dylib0.1.17samtools (Shared library. libbam)link
samtools0.1.19samtoolsRHEL 6.1link
seqtkseqtkCentOS 6.5link
sgaSGA is a de novo genome assembler based on the concept of string graphs.SL6.1linkgoogle-sparsehash bamtools
smlnj110.78Standard ML of New Jersey (abbreviated SML/NJ) is a compilerCentOS6.5link
smrtanalysis-centos2.3.0.140936.p2PacBio SMRT Analysis Pipeline (CentOS binary)CentOS 6.6linkwget
snappy1.1.1Snappy (a fast compressor/decompressor)link
soap-anotherecunknownSOAP ErrorCorrection: Another read correction packageCentOS 6.4link
soap3gpu0.01SOAP3-The alignment program in this package is optimized to work for multi-millions of short reads each time by running a multi-core CPU and the GPU concurrently.SL6.1link
soapdenovo-prepare2.0SOAPdenovo-preparelink
soapdenovo240SOAPdenovo2 (up to 127mer)CentOS 6.4link
soapec2.01SOAPec: Read correction package designed to correct Illumina short reads.CentOS 6.4link
soapgapcloser1.12-r6SOAP GapCloser: Gap closing tool using the abundant pairs of short readsCentOS 6.4link
sparsehash2.0.2sparsehash An extremely memory-efficient hash_map implementationSL6.1link
sprai0.9.9.7Sequencing error correction tool for long reads such as PacBio CLRlink
sratoolkit2.5.2SRAToolkit (for CentOS & Mac)CentOS 6.6link
stacks1.35Stacks: Genetic map builder for RAD sequencingCentOS 6.4link
tcc0.9.25tcc (Tiny C Compiler)link
texlive20120411ptexliveSL6.1link
tgewTiny Grid Engine WrapperCentOS6.3link
thrift0.2.0Thrift (wo/ruby, w/boost)link
tig2.0.3tig (CUI-based git browser)link
tophatTopHat is a fast splice junction mapper for RNA-Seq reads.CentOS 6.6link
trans-abyssTrans-ABySSlink
transdecoderr20131117TransDecoder (Find Coding Regions Within Transcripts)RHEL 6.1link
trf4.07bTandem Repeats Finderlink
trimmomatic0.33Trimmomatic: java based Illumina sequence trimming toolCentOS 6.6link
trinity20131110RNA-Seq De novo Assembly Using TrinityRHEL 6.4link
trinity22.0.6RNA-Seq De novo Assembly Using TrinityCentOS 6.6link
ttyrec1.0.8ttyrec (TTY RECorder)link
ucscuserappsUCSC genome browser related toolsCentOS6.6link
udrUDR: UDT-enabled rsynclink
udt4.11UDP file transfer librarylink
utgb1.5.9UT Genome Browserlink
velvet1.2.10velvet assemblerCentOS 6.6link
viennarna2.1.5viennarnalink
vim7.4VimCentOS 6.4linkpython (if you enable python), ruby (if you enable ruby), lua51 (if you enable lua or luajit), luajit (if you enable luajit)
virtualenvvirtualenv (for Python)CentOS6.4link
wget1.16.3WgetOS X Yosemitelink
wgs8.1Celera Assembler 8.1RHEL 6.4link
wise2.4.1genewise is the homology based gene prediction programlink
x102.5.3X10 langCentOS 6.1link
xerces22.8.0Xerces C++ 2 (XML Parser)link
zlib1.2.8zlibCentOS 6.4link
zsh-lpm-comp1.0Set zsh autocompletion for LPMCentOS 6.4link
zsh-util-envs1.1Set environmental variables and define utility functions for zshSL6.1link