All POD compute servers have identical BioLinux 8 Operating System configurations, which is based Ubuntu 14.04 LTS, plus a number of additional packages we have identified. Some PODs have additional software installed which is unique to that POD.
Standard OS software:
| Software | Description |
|---|---|
| build-essential | gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool |
| emacs, vi, vim, ed | |
| mail, mailx, postfix | |
| perl | |
| python 2 | |
| python 3 | |
| R, R Studio | |
| ruby | |
| samba | |
| screen, tmux | |
| ssh | |
| sudo | |
| tar | |
| wget, curl | |
| whois | |
| zip, unzip |
Additional development tools:
| Software | Description |
|---|---|
| scons | |
| swig | |
| sqlite3 | |
| git, svn, cvs, mercurial |
Additional Python tools:
| Software | Description |
|---|---|
| blaze | |
| cutadapt | |
| dendropy | |
| MACS2 | |
| matplotlib | |
| networkx | |
| nimfa | |
| numpy | |
| pandas | |
| pip | |
| rpy2 | |
| scipy | |
| sklearn | |
| skimage |
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 | |
| ChIPseeker | |
| cummeRbund | |
| DESeq2 | |
| devtools | |
| DEXSeq | |
| GOstats | |
| GO.db | |
| mirbase.db | |
| org.Sc.sgd.db | |
| org.Mm.eg.db | |
| rhdf5 | |
| RIPSeeker | |
| ShortRead | |
| sleuth | |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | |
| TxDb.Hsapiens.UCSC.hg38.knownGene | |
| BSgenome.Hsapiens.UCSC.hg19 |
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 |
|---|---|
| bamtools | SAM/BAM file manipulation |
| bcl2fastq | BCL file manipulation |
| samtools | SAM/BAM file manipulation |
| picard | SAM/BAM file manipulation |
bedtools | BED/GFF file manipulation |
| sra toolkit | SRA file manipulation |
Specialized Sequencing Tools
| Software | Description |
|---|---|
| bwa | Alignment |
| eisen cluster | hierachical & k-means clustering |
| meme_chip | motif analysis toolkit suite |
| art | next generation sequencing read simulator |
RNA Sequencing Tools
| Software | Description |
|---|---|
| express | Expression quantification |
| featurecounts | Counting |
| htseq | Counting |
| kallisto | Expression quantification |
| STAR | Alignment |
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 |
|---|---|
| annovar | Annotation of variants |
| gatk | Human/higher-vertabrate variant detection toolkit |
| MuTect | Somatic Mutations |
| plink | GWAS tools |
| snpeff | Genetic variant annotation and effect prediction |
Evolution Sequencing 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 |
|---|---|
| mauve | |
| orthomcl | NOT YET IMPLEMENTED |
Genome 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 |
|---|---|
| consed | contig assembly tools |
| phrap | contig assembly tools |
| phred | contig assembly tools |
| glimmer | micobial gene annotations |
