Overview
All POD compute servers have identical BioLinux 8 Operating System configurations, which is based Ubuntu 14.04 LTS. See http://environmentalomics.org/bio-linux-software-list/.
A number of additional tools and packages have been installed on all compute servers, as listed below. Note that some tools that have many sub-program binaries are not available on the standard PATH. The /stor/software/opt directory on your system contains installation directories for these tools, which can be added to your PATH as needed.
Some PODs also have additional software installed which is unique to that POD.
Let us know if there is additional software you would like to have installed.
Standard OS Software
| Software | Description |
|---|---|
| build-essential | gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool |
| emacs, vi, vim, ed | text editors |
| mail, mailx, postfix | mail programs |
| perl | perl interpretor |
| python 2 | python version 2 interpretor |
| python 3 | python version 3 interpretor |
| ruby | ruby programming language |
| samba | Windows SMB/CIFS file and printer sharing protocol and applications |
| screen, tmux | Text window managers (multiplexer) |
| ssh | Secure Shell (remote access) |
| sudo | Root access for POD delegates only |
| tar | File archiving utility |
| wget, curl | Remote file/url transfer utilities |
| whois | Whois directory client. |
| gzip, zip, unzip | File compression and archiving tools. |
Standard Third-Party Software
| Software | Description |
|---|---|
| R, R Studio | R and R studio statistical package |
| Matlab | MathWorks Matlab Software |
Additional Development Tools
| Software | Description |
|---|---|
| scons | Software build tool |
| swig | Software development tool |
| sqlite3 | SQL Lite databases |
| git, svn, cvs, mercurial | Version control utilities |
Additional Python Tools
| Software | Description |
|---|---|
| blaze | An interface to query data on different storage systems |
| cutadapt | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads |
| dendropy | phylogenetic computing |
| MACS2 | Model Based Analysis for ChIP-Seq data |
| matplotlib | python 2D plotting library |
| networkx | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. |
| nimfa | Nonnegative matrix factorization |
| numpy | scientific computing with Python |
| pandas | Python Data Analysis Library |
| pip | Python installation program (to install python modules) |
| rpy2 | Python interface to R |
| scipy | Collection of Python software for mathematics, science, and engineering. |
| sklearn | Machine Learning in Python |
| skimage | Image processing in Python |
Additional R Tools
| Software | Description |
|---|---|
| curl | |
| igraph | |
| jpeg | |
| lubridate | |
| mirbase.db | |
| mixdist | |
| network | |
| quantmod | |
| RMySQL | |
| sna | |
| sqldf | |
| tidyr | |
| VGAM | |
| vioplot |
Additional R BioConductor Tools
| Software | Description |
|---|---|
| BSgenome | Efficient genome searching |
| ChIPseeker | annotating ChIP-seq data analysis |
| cummeRbund | analyzing Cufflinks RNA-Seq output |
| DESeq2 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution |
| devtools | Collection of package development tools |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples |
| GOstats | tools for interacting with GO and microarray data |
| GO.db | |
| mirbase.db | |
| org.Sc.sgd.db | |
| org.Mm.eg.db | |
| rhdf5 | provides an interface between HDF5 and R |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments |
| ShortRead | sampling, iteration, and input of FASTQ files |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | |
| TxDb.Hsapiens.UCSC.hg38.knownGene | |
| BSgenome.Hsapiens.UCSC.hg19 | |
| ballgown | Flexible, isoform-level differential expression analysis |
Additional Perl CPAN modules
| Software | Description |
|---|---|
| CGI | |
| DBI | |
| Graph | |
| LWP | |
| Math::Cephes | |
| Net::HTTP | |
| Statistics::Descriptive | |
| Switch | |
| Test::Class | |
| Test::More | |
| Test::Exception | |
| Test::Harness | |
| XML::Simple |
Next Generation Sequencing (NGS) Tools
| Software | Description | Path |
|---|---|---|
| bamtools | SAM/BAM file manipulation | /stor/system/opt/gitdir/bamtools/bin/bamtools |
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq |
| samtools | SAM/BAM file manipulation | /usr/bin/samtools /usr/bin/samtools_0.1.18 /usr/bin/samtools-1.3 |
| picard | SAM/BAM file manipulation | /stor/system/opt/picard-tools-1.141 /stor/system/opt/picard-tools-2.5.0 |
bedtools | BED/GFF file manipulation | /usr/bin/bedtools-2.17.0 /usr/bin/bedtools-2.25.0 |
| sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 |
| bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools
| Software | Description | Path |
|---|---|---|
| express | Expression quantification | /usr/bin/express |
| featurecounts | Counting | /usr/bin/featureCounts |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 |
| kallisto | Expression quantification | /usr/bin/kallisto |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong |
| MultiQC | Report Generation | /usr/bin/multiqc |
| RNA-SeQC | QC of RNA-seq alignments. To run this Java program: java -jar /stor/system/opt/rnaseqc/RNA-SeQC_v1.1.8.jar <other options> | /stor/system/opt/rnaseqc |
| hisat | Spliced alignment for mapping RNA-seq reads | /stor/system/opt/hisat-0.1.6-beta |
| hisat2 | Align NGS reads (both DNA and RNA) against a reference genome | /stor/system/opt/hisat2-2.0.5/ |
Specialized NGS Tools
| Software | Description | Path |
|---|---|---|
| MultiQC | Report Generation | /usr/bin/multiqc |
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen |
| meme suite | motif analysis | /stor/system/opt/meme_4.11.2 |
| meme_chip | motif analysis suite for ChIP-seq | /stor/system/opt/software/meme-chip/4.11.2/ |
| art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD |
Variant Analysis Tools
NB: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Iyer PODs.
| Software | Description | Path |
|---|---|---|
| annovar | Annotation of variants | /stor/system/opt/annovar/ |
| gatk | Human/higher-vertabrate variant detection toolkit | /stor/system/opt/gatk-3.6/ |
| MuTect | Somatic Mutations | /stor/system/opt/gatk-3.6/ /stor/system/opt/mutect/ |
| plink | GWAS tools | /usr/bin/plink |
| snpeff | Genetic variant annotation and effect prediction | /stor/system/opt/snpEff |
Evolutionary Analysis Tools
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF POD.
| Software | Description | Path |
|---|---|---|
| mauve | ||
| orthomcl | NOT YET IMPLEMENTED |
Genome/Transcriptome Assembly Tools
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF POD.
| Software | Description | Path |
|---|---|---|
| consed | contig assembly tools | /usr/local/genome/consed/ |
| phrap | contig assembly tools | /usr/local/genome/bin/ |
| phred | contig assembly tools | /usr/local/genome/bin/ |
| glimmer | micobial gene annotations | /usr/bin/glimmer2 /usr/bin/build-icm /usr/bin/extract /usr/bin/long-orfs |
Special POD software
The following software is available only on specific PODs or nodes of a pod.
| Software | Description | Location | Path |
|---|---|---|---|
| bam2fastq | Iyer POD | /stor/system/opt/bam2fastq-1.1.0/ | |
| docker | Marcotte POD | ||
| irodsfs | Not yet fully supported | gsafcbig01 | /mnt/corral |
| jupiterhub | Python Notebook Server | gsafcbig01 gsafcbig02 ccbbcomp02 iyercomp04 | https://gsafcbig01.ccbb.utexas.edu/ |
| R Server | R Studio Web Interface | lambcomp01 iyercomp03 marccomp01 wcarcomp01 | https://lambcomp01.ccbb.utexas.edu/ |
| R caTools | Iyer POD | ||
| R snow | Iyer POD | ||
| R phantompeakqualtools | Iyer POD | ||
| R NCIS | Iyer POD |