...
| 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 | ||
|---|---|---|---|---|
| mauve | ||||
| orthomcl | NOT YET IMPLEMENTED |
Genome/Transcriptome Assembly Tools
...
| 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 |