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Software
$/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
$/gscratch/srlab/programs/bin
argparse.py bowtie2 bsmap cutadapt fastqc multiqc quast.py README.txt samtools trim_galore
This directory contains symlinks (i.e. shortcuts) to various programs and will simplify adding programs to your "system" $PATH (for many programs, this is not necessary, so you may not need/want to bother).
To add this directory (and it's programs) to your system $PATH, type the following in your Mox login node command prompt:
printf "%s\n%s" "# Prepend bioinformatics stuff to PATH" "PATH=/gscratch/srlab/programs/bin:$PATH" >> ~/.bash_profile
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).
You should also add our custom modules directory to your ~/.bashrc file. Modules are useful for certain software that has specific $PATH requirements. 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).