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Let us know if there is additional software you would like to have installed.
Web-based application R Studio and Python software
The following web application software is available on all PODs. Accessing a POD node with your web browser will take you to an application login page where your BRCF account credentials can be used to access the application's web interface. Your default directory will be your Home directory. See Home directory quotas for important storage-quota related information. See also About R and R Studio Server.
| Software | Description | Access |
|---|---|---|
| JupyterHub Server | Python Notebook Server | Available on all compute servers https://<server_name>.ccbb.utexas.edu |
| R Studio Server | R Studio Web Interface |
Standard OS Software (where in repo?)
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| Software | Description | in perl.pp or cqb-maker? | |||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bit::Vector | y | ||||||||||||||||||||||||||||||||||||||||
| CGI | y | DBI | y | DBD::SQLite | y | File::Which | y | forks | y | forks::shared | y | Graph | y | IO::All | y | IO:Prompt | y | LWP | y | Math::Cephes | y | Module::Build | y | Net::HTTP | y | Perl::Unsafe::Signals | y | Statistics::Descriptive | y | Switch | y | Test::Class | y | Test::More | y | Test::Exception | y | Test::Harness | y | XML::Simple | y |
Next Generation Sequencing (NGS) Tools (cqbprofile/manifest/next_gen_sequencing_client.pp)
| Software | Description | Path | in next_gen_sequencing_client.pp | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bamtools | SAM/BAM file manipulation | /stor/system/opt/gitdir/bamtools/bin/bamtools | y | |||||||||||
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq | y | |||||||||||
| deeptools | y | enabrowsertools | y | hisat | y | fastq_screen | guppy | y | samtools | SAM/BAM file manipulation | /usr/bin/samtools /usr/bin/samtools_0.1.18 /usr/bin/samtools-1.3 | picardy | ||
| DBI | y | |||||||||||||
| DBD::SQLite | y | |||||||||||||
| File::Which | y | |||||||||||||
| forks | y | |||||||||||||
| forks::shared | y | |||||||||||||
| Graph | y | |||||||||||||
| IO::All | y | |||||||||||||
| IO:Prompt | y | |||||||||||||
| LWP | y | |||||||||||||
| Math::Cephes | y | |||||||||||||
| Module::Build | y | |||||||||||||
| Net::HTTP | y | |||||||||||||
| Perl::Unsafe::Signals | y | |||||||||||||
| Statistics::Descriptive | y | |||||||||||||
| Switch | y | |||||||||||||
| Test::Class | y | |||||||||||||
| Test::More | y | |||||||||||||
| Test::Exception | y | |||||||||||||
| Test::Harness | y | |||||||||||||
| XML::Simple | y |
Next Generation Sequencing (NGS) Tools (cqbprofile/manifest/next_gen_sequencing_client.pp)
| Software | Description | Path | in next_gen_sequencing_client.pp | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bamtools | SAM/BAM file manipulation | /stor/system/opt/picard-tools-1.141 /stor/system/opt/picard-tools-2.5.0 | y | bedtools | BED/GFF file manipulation/gitdir/bamtools/bin/bamtools | y | ||||||
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq | y | |||||||||
| deeptools | y | |||||||||||
| enabrowsertools | y | |||||||||||
| hisat | y | |||||||||||
| fastq_screen | ||||||||||||
| guppy | y | |||||||||||
| samtools | SAM/BAM file manipulation | /usr/bin/samtools /usr/bin/bedtools-2.17.0samtools_0.1.18 /usr/bin/bedtoolssamtools-21.25.03 | y | samtools | y | |||||||
| scalangs | y | sra toolkit | SRApicard | SAM/BAM file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 | y | stringtie | y | bwa | Alignment | /usr/bin/bwa /usr/bin/bwa-0.5.9 /usr/bin/bwa5picard-tools-1.141 /stor/system/opt/picard-tools-2.5.0 | y |
bedtools | BED/GFF file manipulation | /usr/bin/bwabedtools-0.6.2 /usr/bin/bwa6 |
RNA Sequencing Tools (cqbprofile/manifest/rna_sequencing_client.pp)
| Software | Description | Path | in rna_sequencing_client.pp | augustus | y | busco | y | cellranger | y | cufflinks | y | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| express | Expression quantification | /usr/bin/express | y | ||||||||||||
| fastqc | y | featurecounts | Counting.17.0 /usr/bin/bedtools-2.25.0 | y | |||||||||||
| samtools | y | ||||||||||||||
| scalangs | y | ||||||||||||||
| sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 | y | ||||||||||||
| stringtie | y | ||||||||||||||
| bwa | Alignment | /usr/bin/ featureCounts | y | htseq | Counting | /stor/system/opt/HTSeq bwa | y | kallisto | Expression quantification | 5.9 | y | STAR | Alignment | bwa5 bwa-0.6.2 /bwa6 |
RNA Sequencing Tools (cqbprofile/manifest/rna_sequencing_client.pp)
| Software | Description | Path | in rna_sequencing_client.pp | |||||
|---|---|---|---|---|---|---|---|---|
| augustus | y | |||||||
| busco | y | |||||||
| cellranger | y | |||||||
| tophatcufflinks | y | |||||||
| MultiQCexpress | Report GenerationExpression quantification | /usr/bin/multiqcexpress | y | RNA-SeQC | QC of RNA-seq alignments.||||
| /stor/system/opt/rnaseqc | y | salmon | y | hisat | Spliced alignment for mapping RNA-seq readsfastqc | y | ||
| featurecounts | Counting | /usr/bin/featureCounts | y | |||||
| htseq | Counting | /stor/system/opt/hisatHTSeq-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 (specialized_sequencing_client.pp)
| Software | Description | Path | in specialized_sequencing_client.pp | ||
|---|---|---|---|---|---|
| BWA | y | bwa_mem26.1p1 | y | ||
| kallisto | Expression quantification | /usr/bin/kallisto | y | ||
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong | y | ||
| tophat | y | ||||
| MultiQC | Report Generation | /usr/bin/multiqc | |||
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen | y | ||
| imageJ | y | meme suite | motif analysis | y | |
| 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/meme_4.11.2 | meme_chip | motif analysis suite for ChIP-seqrnaseqc | y |
| salmon | y | ||||
| hisat | Spliced alignment for mapping RNA-seq reads | /stor/system/opt/software/meme-chip/4.11.2/ | y | ||
| art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD | y |
Variant Analysis Tools (variant_analysis_client.pp)
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| 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 (specialized_sequencing_client.pp)
| Software | Description | Path | in variantspecialized_analysissequencing_client.pp | |
|---|---|---|---|---|
| annovar | Annotation of variants | /stor/system/opt/annovar/ | y | |
| gatk | Human/higher-vertabrate variant detection toolkit | /stor/system/opt/gatk-3.6/ | y | |
| MuTect | Somatic Mutations||||
| BWA | y | |||
| bwa_mem2 | y | |||
| MultiQC | Report Generation | /usr/bin/multiqc | ||
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen | y | |
| imageJ | y | |||
| meme suite | motif analysis | /stor/system/opt/gatk-3.6/meme_4.11.2 | ||
| meme_chip | motif analysis suite for ChIP-seq | /stor/system/opt/mutectsoftware/meme-chip/4.11.2/ | y | plink |
| art | next generation sequencing read simulator | /usr/bin/plink | y | |
| snpeff | Genetic variant annotation and effect prediction | /stor/system/opt/snpEff | y |
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| art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD | y |
Variant Analysis Tools (variant_analysis_client.pp)
NoteNB: These tools are only available on select PODs. At this time of this writing, it included the GSAF PODand Iyer PODs.
| Software | Description | Path | in evolutionvariant_sequencinganalysis_client.pp? |
|---|---|---|---|
| annovary | Annotation of variants |
Genome/Transcriptome Assembly Tools genome_client.pp
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Educational PODs.
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Web-based application R Studio and Python software
The following web application software is available on all PODs. Accessing a POD node with your web browser will take you to an application login page where your BRCF account credentials can be used to access the application's web interface. Your default directory will be your Home directory. See Home directory quotas for important storage-quota related information. See also About R and R Studio Server.
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Available on all compute servers
https://<server_name>.ccbb.utexas.edu
(e.g. https://gsafcomp01.ccbb.utexas.edu)
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| /stor/system/opt/annovar/ | y | ||
| gatk | Human/higher-vertabrate variant detection toolkit | /stor/system/opt/gatk-3.6/ | y |
| MuTect | Somatic Mutations | /stor/system/opt/gatk-3.6/ /stor/system/opt/mutect/ | y |
| plink | GWAS tools | /usr/bin/plink | y |
| snpeff | Genetic variant annotation and effect prediction | /stor/system/opt/snpEff | y |
Evolutionary Analysis Tools (evolution_sequencing_client.pp)
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF POD.
| Software | Description | Path | in evolution_sequencing_client.pp? |
|---|---|---|---|
| mauve | y |
Genome/Transcriptome Assembly Tools genome_client.pp
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Educational PODs.
| Software | Description | Path | in genome_client.pp |
|---|---|---|---|
| consed | contig assembly tools | /usr/local/genome/consed/ | y |
| phrap | contig assembly tools | /usr/local/genome/bin/ | y |
| phred | contig assembly tools | /usr/local/genome/bin/ | y |
| glimmer | micobial gene annotations | /usr/bin/glimmer2 /usr/bin/build-icm /usr/bin/extract /usr/bin/long-orfs | y |
POD-specific software
The following software is available only on specific PODs or nodes of a pod.
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