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 simple 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