Skip to content

Software

Program locations

The majority of programs can be found in:

$/gscratch/srlab/programs/

(Ana) conda programs are a bit more difficult to track down, but try looking in these two locations:

/gscratch/srlab/programs/anaconda3/bin/

Modules

Modules are a relatively simply way to add programs to your system $PATH

A module is a text file. Here's an example from cat /gscratch/srlab/programs/modules/maker-3.01.03.module:

#%Module1.0
proc ModulesHelp { } {
        puts stderr "\tAdds MAKER dependencies to environment."
}

module-whatis "Adds MAKER dependencies to environment."

setenv          ZOE             /gscratch/srlab/programs/snap-2013-11-29/Zoe
setenv          AUGUSTUS_CONFIG_PATH             /gscratch/srlab/programs/Augustus-3.3.2/config
prepend-path    PATH            /gscratch/srlab/programs/exonerate-2.2.0-x86_64/bin
prepend-path    PATH            /gscratch/srlab/programs/ncbi-blast-2.10.1+/bin
prepend-path    PATH            /gscratch/srlab/programs/snap-2013-11-29
prepend-path    PATH            /gscratch/srlab/programs/RepeatMasker-4.1.0

There are two lines that describe what the module does (e.g. Adds MAKER dependencies to environment.)

Those are followed by setting some environmental variables and adding other programs to the system $PATH needed by the MAKER program.

Loading modules

There are many pre-made modules available for anyone to use at any time. List them like so:

module avail

Modules preceded by contrib/ are modules created by other Mox users outside of the Roberts Lab.

The remaining modules are those created by Mox UW-IT staff and primarily utility applications.

To run (i.e. load) a module (replace <module_name> with the module name or full path to module file):

module load <module_name>

You can add our custom modules directory to your ~/.bashrc file. This will allow you to load a module by calling just the the name of the module file without the need to call the full module paht. See the modules directory for more info on what custom modules are available (/gscratch/srlab/programs/modules).

printf "\n%s\n%s\n%s" "# Prepend custom modules to system ${MODULEPATH}" "MODULEPATH=/gscratch/srlab/programs/modules:${MODULEPATH}" "export MODULEPATH" \
>> ~/.bashrc

To make the above command active, type bash at the command prompt (you only need to do this one time; your changes will be loaded each time you login).

Available Programs

Below is the current list of programs available on Mox. It's very dynamic, so please check the contents of $/gscratch/srlab/programs periodically. If you need some other/new programs, please refer to the program installation instructions or feel free to ask Sam.

$/gscratch/srlab/programs
2bRAD_GATK            DRAP                   macau                    perl              smrtanalysis_2.3.0.140936.run
anaconda3             exonerate-2.2.0-x86_64             maker-2.31.10                picard_2.18.4         snap-2013-11-29
argparse-1.4.0            express-1.5.1-linux_x86_64         maker-3.01.03                picard-2.9.1          SOAPdenovo2
Augustus-3.3.2            FastaIndex                 MaSuRCA-3.2.3                pigz-2.4              SOAPec_bin_v2.03
bamtools-2.5.1            fastp-0.20.0               mawk-1.3.4-20190203              pilon             SPAdes-3.13.0-Linux
bbmap_38.34           FastQC-0.11.5              mdust                    pitchfork             SparseAssembler
bcftools-1.9              fastqc_v0.11.8                 megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin  platanus_1.2.4            sqlite
bcl2fastq-v2.20           fastqc_v0.11.9                 MEGAN6                   pstl              sratoolkit.2.10.6-centos_linux64
bedtools-2.27.1           freebayes-v.1.3.0-1            MEGAN-6.18.3                 pyfaidx-0.5.5.2           SSPACE-LongRead_v1-1
bin               gapcloser-1.12                 MEGAN_Community_unix_6_17_0.sh       pyScaf                SSPACE-STANDARD-3.0_linux-x86_64
Bismark-0.19.0            GARM_v0.7.5                MEGAN_Community_unix_6_18_3.sh       quast-4.5             stacks-2.41
Bismark-0.21.0            GATK                   MetaGeneMark_linux_64_3.38           R-3.6.2               STAR-2.7.6a
Bismark-0.21.0_dev        gcc                    Metassembler                 racon             stringtie-1.3.6.Linux_x86_64
Bismark-0.22.3            get-pip.py                 miniconda3                   rainbow_2.0.4         stringtie-2.1.4.Linux_x86_64
blast-2.2.17              gffread-0.11.4.Linux_x86_64        minimap2-2.17_x64-linux              reago-1.1-release-2015.12.18  supernova-2.0.0
blat-v36x2            git-sym                    modules                      redundans             tbb
blat-v36x5            graphviz-2.40.1                mummer                   RepeatMasker-4.1.0        tguenther-bayenv2_public-2b2b7f20bb62
bowtie2-2.1.0             gt-1.5.10-Linux_x86_64-64bit-complete  MUMmer3.23                   resources             tmhmm-2.0c
bowtie2-2.3.4.1-linux-x86_64  hisat2-2.1.0               mummer-4.0.0beta2                rmblast-2.10.0            transdecoder
bowtie2-2.3.5.1-linux-x86_64  hisat2-2.2.0               NanoPlot-1.29.1                  RNAMMER-1.2           TransDecoder-v5.3.0
bowtie2-2.4.1-linux-x86_64    hmmer-2.3                  ncbi-blast-2.10.1+               RSEM-1.3.3            TransDecoder-v5.5.0
bsmap-2.89            hmmer-3.1b2                ncbi-blast-2.6.0+                salmon-0.11.2-linux_x86_64    tree-1.8.0
busco-v3              hmmer-3.2.1                ncbi-blast-2.8.1+                salmon-1.1.0_linux_x86_64     trf409.linux64
bwa-0.7.15            hmmer-3.3                  ncbi-blast-2.8.1+_orginal            salmon-1.2.1_linux_x86_64     TrimGalore-0.4.5
bwa-0.7.17            htslib-1.9                 networkx-1.11                samtools-1.10         TrimGalore-0.6.6
canu                  infernal-1.1.1                 networkx2                    samtools-1.4          Trimmomatic-0.33
cd-hit-v4.8.1-2019-0228       interproscan-5.31-70.0             nseg                     samtools-1.9          Trimmomatic-0.36
celera                jellyfish-1.1.11               ont-guppy_3.4.4                  scripts               trinityrnaseq-v2.9.0
cmake-3.12.1              jellyfish-2.2.10               ont-guppy_4.0.15_linux64             sedef             Trinity-v2.8.3
dDocent-2.7.8             jellyfish-2.3.0                parallel-20180822                seqtk-1.3             Trinotate-v3.1.1
decorator-4.0.11          jsoncpp-1.8.4              parallel-20190922                setuptools-36.0.1         Trinotate-v3.2.0
detonate-1.11             kmergenie-1.7048               pblat-2.1                    Sibelia-3.0.7-Source      vcflib
diamond-0.9.26            krakenuniq-0.5.8               PBSuite                      signalp-4.1           vcftools-0.1.16
diamond-0.9.29            last-852                   pear-0.9.11-linux-x86_64             signalp-5.0b          wtdbg-2.1_x64-linux
diamond-2.0.4             likelybin-0.1.0                pecan                    simuPOP-1.1.10.9