SciCodePile/SciCode-Domain-Code
DATA1: Domain-Specific Code Dataset Dataset Overview DATA1 is a large-scale domain-specific code dataset focusing on code samples from interdisciplinary fields such as biology, chemistry, materials science, and related areas. The dataset is collected and organized from GitHub repositories, covering 178 different domain topics with over 1.1 billion lines of code. Dataset Statistics Total Datasets: 178 CSV files Total Data Size: ~115 GB Total Lines… See the full description on the dataset page: https://huggingface.co/datasets/SciCodePile/SciCode-Domain-Code.
42.4k
1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"AlphaFold","oist/BioinfoUgrp","Nextflow.md",".md","4676","168","Nextflow3========4 5A DSL for data-driven computational pipelines <http://nextflow.io>.6 7In 2022, _Nextflow_ had a backwards-incompatible change that depreacated an old8syntax called _DSL1_ in favor of the _DSL2_ syntax. We still provide the old9version `21.10.6` in the `Nextflow` module on _deigo_. Newer versions are in10the `Nextflow2` module. To use a _DSL1_ pipeline with the `Nextflow2` module,11pass the `-dsl1` flag to the `nextflow` program.12 13The `Nextflow2` module also limits the use of memory by setting the environment14variable `NXF_OPTS` to `-Xms500M -Xmx2G`. Please contact us or open an issue15if you hit the limit.16 17 18Installation on deigo19---------------------20 21See also <https://groups.oist.jp/scs/install-software-your-unit>.22 23### Release or edge versions from GitHub24 25Source: https://github.com/nextflow-io/nextflow26 27```28APP=Nextflow229MODROOT=/bucket/BioinfoUgrp/Other30APPDIR=$MODROOT/$APP31VER=25.10.232mkdir -p $APPDIR/$VER/bin33cd $APPDIR/$VER34wget https://github.com/nextflow-io/nextflow/releases/download/v${VER}/nextflow-${VER}-dist35mv nextflow-${VER}-dist bin/nextflow36chmod 775 bin/nextflow37mkdir -p $MODROOT/$APP/modulefiles/38cd $MODROOT/$APP/modulefiles/39cat <<'__END__' > $VER.lua40-- Default settings41local modroot = ""/bucket/BioinfoUgrp/Other""42local appname = myModuleName()43local appversion = myModuleVersion()44local apphome = pathJoin(modroot, myModuleFullName())45 46-- Package information47whatis(""Name: ""..appname)48whatis(""Version: ""..appversion)49whatis(""URL: ""..""https://github.com/nextflow-io/nextflow/releases"")50whatis(""Category: ""..""bioinformatics"")51whatis(""Keywords: ""..""pipeline, SLURM"")52whatis(""Description: "".."" Data-driven computational pipelines."")53 54help([[Nextflow version downloaded from GitHub55 56See https://www.nextflow.io/ for help.]])57 58-- Package settings59depends_on(""singularity"")60depends_on(""java-jdk/17"")61setenv(""NXF_OPTS"", ""-Xms500M -Xmx2G"")62prepend_path(""PATH"", apphome..""/bin"")63__END__64```65 66nf-test67=======68 69Testing framework for Nextflow pipelines (<https://www.nf-test.com/>).70 71Installation on deigo72---------------------73 74```75APP=nf-test76MODROOT=/bucket/BioinfoUgrp/Other77APPDIR=$MODROOT/$APP78VER=0.9.279mkdir -p $APPDIR/$VER/bin80cd $APPDIR/$VER81wget https://github.com/askimed/nf-test/releases/download/v${VER}/nf-test-${VER}.tar.gz82pushd bin83tar xvfz ../nf-test-${VER}.tar.gz84chmod 775 nf-test85chmod 664 nf-test.jar86popd87rm nf-test-${VER}.tar.gz88cd $MODROOT/modulefiles/89mkdir -p $APP90cat <<'__END__' > $APP/$VER.lua91-- Default settings92local modroot = ""/bucket/BioinfoUgrp""93local appname = myModuleName()94local appversion = myModuleVersion()95local apphome = pathJoin(modroot, myModuleFullName())96 97-- Package information98whatis(""Name: ""..appname)99whatis(""Version: ""..appversion)100whatis(""URL: ""..""https://github.com/askimed/nf-test/releases"")101whatis(""Category: ""..""bioinformatics"")102whatis(""Keywords: ""..""pipeline, SLURM"")103whatis(""Description: ""..""Testing framework for Nextflow pipelines."")104 105help([[nf-test version downloaded from GitHub106 107See https://www.nf-test.com/ for help.]])108 109-- Package settings110depends_on(""Nextflow2"")111prepend_path(""PATH"", apphome..""/bin"")112__END__113```114 115nf-core116=======117 118Python package with helper tools for the nf-core community (<https://nf-co.re/docs/nf-core-tools>).119 120To install a new latest version, update the `VER` variable below and run the commands.121 122```123ml purge124ml bioinfo-ugrp-modules Nextflow2125ml python/3.11.4126APP=nf-core127MODROOT=/bucket/BioinfoUgrp/Other128APPDIR=$MODROOT/$APP129VER=3.5.1130mkdir -p $APPDIR/$VER131cd $APPDIR/$VER132PYTHONUSERBASE=$(pwd) pip3 install --no-warn-script-location --user $APP 133PYTHONUSERBASE=$(pwd) pip3 install --no-warn-script-location --user pre-commit134cd $MODROOT/$APP/modulefiles/135cp 3.1.2.lua ${VER}.lua136```137 138Contents of 3.1.2.lua:139 140```141-- Default settings142local modroot = ""/bucket/BioinfoUgrp/Other""143local appname = myModuleName()144local appversion = myModuleVersion()145local apphome = pathJoin(modroot, myModuleFullName())146-- setenv(""Nextflow_MOD_HOME"", apphome)147-- setenv(""Nextflow_MOD_VERSION"", appversion)148 149-- Package information150whatis(""Name: ""..appname)151whatis(""Version: ""..appversion)152whatis(""URL: ""..""https://nf-co.re/docs/nf-core-tools"")153whatis(""Category: ""..""bioinformatics"")154whatis(""Keywords: ""..""pipeline, SLURM"")155whatis(""Description: "".."" Python package with helper tools for the nf-core community."")156 157help([[nf-core tools installed with pip158 159See https://nf-co.re/ for help.]])160 161-- Package settings162depends_on(""singularity"")163prepend_path(""PATH"", apphome..""/bin"")164prepend_path(""PYTHONPATH"", apphome..""/lib/python3.11/site-packages/"")165depends_on(""Nextflow2"")166depends_on(""python/3.11.4"")167depends_on(""Other/nf-test"")168```169","Markdown"
170"AlphaFold","oist/BioinfoUgrp","DebianMedModules.md",".md","6201","156","Debian Med modules171==================172 173The [Debian Med](https://www.debian.org/devel/debian-med/) project packages174bioinformatics and other medically relevant software for the175[Debian](https://www.debian.org/intro/about) operating system. We collect176many of them in a [Singularity](https://sylabs.io/) container and create one177module per package on Deigo.178 179For users180---------181 182```183ml bioinfo-ugrp-modules DebianMed184ml av185```186 187Enjoy !188 189 190For developers191--------------192 193### Docker image194 195See [oist/BioinfoUgrp_DebianMed_Images](https://github.com/oist/BioinfoUgrp_DebianMed_Images)196on how to create a Docker image with [GitHub actions](https://docs.github.com/en/actions).197 198### Create a new Singularity image199 200Pull the Docker image built on GitHub.201 202```203export DEBVERSION=13.0-1204singularity pull DebianMed_${DEBVERSION}.sif docker://ghcr.io/oist/bioinfougrp_debianmed_images:${DEBVERSION}205```206 207### Generate all the modules208 209Make sure the module and modulefiles created are writable for the group:210 211```212umask 002213```214 215Generate a list of all the bioinformatics packages recommended by the med-bio and med-cloud metapackages:216 217```218PKGLIST=$(./DebianMed_$DEBVERSION.sif apt show med-bio med-cloud |219 grep Recommends | 220 sed 's/ |/,/'g | # Sanitize pipe symbols representive alternatives221 cut -d' ' -f2- | # Remove 'Recommends: '222 sed -e 's/, /\n/g' | # Make it a space-separated pacakge list 223 sort -u | # Remove duplicates and in the next command, remove R packages224 grep -v -e r-cran -e r-bioc -e r-other )225```226 227Create the modules228 229```230ln -s DebianMed_${DEBVERSION}.sif debalamod.sif231debalamod.sif cp /debalamod .232chmod 775 debalamod233for package in $PKGLIST source-highlight234do235 ./debalamod $package236done237```238 239After creating a new module, if it is not seen by `ml av`, delete the cache:240 241```242rm -rf ~/.lmod.d/.cache243```244 245### `biosyntax-less` module246 247This module was generated by hand as it needs complex setting of environment variables.248 249```250mkdir -p /bucket/BioinfoUgrp/DebianMed/$DEBVERSION/modules/biosyntax-less/1.0.0b-2251cd /bucket/BioinfoUgrp/DebianMed/$DEBVERSION/modules/biosyntax-less/1.0.0b-2252cat > src-hilite-lesspipe-bio.sh <<__END__253#!/bin/sh254LC_ALL=C singularity exec /bucket/BioinfoUgrp/DebianMed/$DEBVERSION/DebianMed_$DEBVERSION.sif /usr/share/source-highlight/src-hilite-lesspipe-bio.sh ""\$@"" 255__END__256chmod 775 src-hilite-lesspipe-bio.sh257mkdir -p /bucket/BioinfoUgrp/DebianMed/$DEBVERSION/modulefiles/biosyntax-less/258cat > /bucket/BioinfoUgrp/DebianMed/$DEBVERSION/modulefiles/biosyntax-less/1.0.0b-2.lua <<__END__259-- Default settings260local modroot = ""/bucket/BioinfoUgrp/DebianMed/$DEBVERSION""261local appname = myModuleName()262local appversion = myModuleVersion()263local apphome = pathJoin(modroot, ""modules"", ""biosyntax-less"", appversion)264 265-- Package information266whatis(""Name: ""..appname)267whatis(""Version: ""..appversion)268whatis(""URL: ""..""https://github.com/oist/BioinfoUgrp"")269whatis(""Category: "".."" bioinformatics"")270whatis(""Keywords: "".."" Bioinformatics, Debian"")271whatis(""Description: "".."" Syntax Highlighting for Computational Biology"")272 273help([[This module runs from Singularity image of Debian Med.274Please contact the Bioinfo user group for details.]])275 276-- Package settings277depends_on(""singularity"", ""source-highlight"")278 279-- Adatpted from /usr/share/doc/biosyntax-less/rc_append.txt280 281pushenv(""HIGHLIGHT"", ""/usr/share/source-highlight"")282pushenv(""LESSOPEN"", ""| "" .. apphome .. ""/src-hilite-lesspipe-bio.sh %s"")283pushenv(""LESS"", "" -R "")284 285set_alias(""less"", ""less -NSi -# 10"")286-- -N: add line numbers287-- -S: don't wrap lines (force to single line)288-- -# 10: Horizontal scroll distance289 290-- Explicit call of <file format>-less for piping data291-- i.e: samtools view -h aligned_hits.bam | sam-less292-- Core syntaxes (default)293set_alias(""clustal-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/clustal.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/fasta.style | less"")294set_alias(""bed-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/bed.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/sam.style | less"")295set_alias(""fa-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/fasta.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/fasta.style | less"")296set_alias(""fq-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/fastq.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/fasta.style | less"")297set_alias(""gtf-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/gtf.lang --outlang-def=\$HIGHLIGHT/bioSyntax-vcf.outlang --style-file=\$HIGHLIGHT/vcf.style | less"")298set_alias(""pdb-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/pdb.lang --outlang-def=\$HIGHLIGHT/bioSyntax-vcf.outlang --style-file=\$HIGHLIGHT/pdb.style | less"")299set_alias(""sam-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/sam.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/sam.style | less"")300set_alias(""vcf-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/vcf.lang --outlang-def=\$HIGHLIGHT/bioSyntax-vcf.outlang --style-file=\$HIGHLIGHT/vcf.style | less"")301set_alias(""bam-less"", ""sam-less"")302 303-- Auxillary syntaxes (uncomment to activate)304set_alias(""fai-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/faidx.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/sam.style | less"")305set_alias(""flagstat-less"", ""source-highlight -f esc --lang-def=\$HIGHLIGHT/flagstat.lang --outlang-def=\$HIGHLIGHT/bioSyntax.outlang --style-file=\$HIGHLIGHT/sam.style | less"")306__END__307```308 309### Finally make the modules available310 311Test them before !312 313```314cat > /apps/.bioinfo-ugrp-modulefiles81/DebianMed/$DEBVERSION.lua <<__END__315-- Setup Modulepath for packages built by this compiler316-- local mroot = os.getenv(""MODULEPATH_ROOT"")317prepend_path(""MODULEPATH"", ""/bucket/BioinfoUgrp/DebianMed/$DEBVERSION/modulefiles"")318__END__319```320 321## TODO322 323 - Parse description from Debian package324 - Export man pages and add MANPATH to the Lua module.325","Markdown"
326"AlphaFold","oist/BioinfoUgrp","DataBases.md",".md","6966","163","# Databases327 328## Taxified BLAST databases329The following databases were constructed using ncbi-blast v2.10.0+. The module `ncbi-blast/2.10.0+` has to be loaded in order to use these databases.330- NCBI NT and NR databases (release 238) : `ml DB/blastDB/ncbi/238`. To be used with the arguments `nt` or `nr` supplied to `-db` in the commands of your scripts. Example script to get a taxified blast report:331```332module load ncbi-blast/2.10.0+333module load DB/blastDB/ncbi/238334WORKDIR=""$PWD""335FASTA=FULL/PATH/TO/YOUR/FASTA/FILE336blastn -task megablast -db nt -query $FASTA -num_threads ${SLURM_CPUS_PER_TASK} -out ${WORKDIR}/megablastn.out \337 -outfmt '6 qseqid bitscore evalue length qlen qcovs pident sseqid sgi sacc staxid ssciname scomname stitle sseq' \338 -max_target_seqs 1339```340- Swiss-Prot (version 2020_06): `ml DB/blastDB/sprot/2020_06`341- UniRef90 (version 2020_06): `ml DB/blastDB/uniref90/2020_06`342 343## Taxified DIAMOND databases344The following databases were constructed using DIAMOND v2.0.4.142. The module `Other/DIAMOND/2.0.4.142` has to be loaded in order to use them.345- the NCBI-NR database (release 238): `ml DB/diamondDB/ncbi/238`346- Swiss-Prot (version 2020_06): `ml DB/diamondDB/sprot/2020_06`347- UniRef90 (version 2020_06): `ml DB/diamondDB/uniref90/2020_06`348 349Unlike ncbi-blast, DIAMOND requires full path of the databases. The database module automatically create an environment variable ""DIAMONDDB"" which specifies full path to the DIAMOND database. So you need to prepend `${DIAMONDDB}` to the name of database. 350Example script to run diamond with the database module:351```352# load ncbi database for DIAMOND (proper version of DIAMOND is automatically loaded)353module load DB/diamondDB/ncbi/238354 355# check the loaded DIAMOND version and ${DIAMONDDB} variable356diamond --version357echo ${DIAMONDDB}358 359# run diamond search360WORKDIR=""$PWD""361FASTA=FULL/PATH/TO/YOUR/FASTA/FILE362diamond blastp -db ${DIAMONDDB}/nr -q $FASTA -p ${SLURM_CPUS_PER_TASK} -out ${WORKDIR}/diamond.blastp.out -outfmt 6363```364 365## GTDB DIAMOND Database (r226)366 367The Genome Taxonomy Database (GTDB) DIAMOND database was constructed using DIAMOND v2.1.11. The ```bioinfo-ugrp-modules``` module needs to be loaded in order to use it. 368 369### Available as Module370 371Load the module to access the database path: `module load DB/diamondDB/GTDB/r226`372 373 374**Use case**: Fast sequence similarity searches against GTDB reference genomes (BLAST-like functionality)375 376##### Example script377 378```bash379# Load bioinfo-user group modules380module load bioinfo-ugrp-modules381# Load GTDB database module382module load DB/diamondDB/GTDB/r226383 384# Optional: set variables for output directory and fasta files path385OUTDIR=/path/to/ouput/directory386FASTA=/path/to/fasta/files387 388# Create output directory if it does not exist389mkdir -p ${OUTDIR}390 391# Run search392diamond blastp -d ${DIAMONDDB}/gtdb.dmnd -q ${FASTA} -p 4 -o ${OUTDIR}393 394```395 396## GTDB-Tk r226 Reference Data397 398The GTDB-Tk r226 reference data package contains the auxiliary files required for taxonomic classification of bacterial and archaeal genomes. This is **the database only** - the GTDB-Tk software itself is not installed as a module, but is available through nf-core pipeline containers.The ```bioinfo-ugrp-modules``` module needs to be loaded in order to use it. 399 400 401**Use case**: Provides the reference database path for GTDB-Tk when running nf-core pipelines (e.g., nf-core/mag)402 403 404### Available as Module405 406Load the module to access the database path: ```module load DB/GTDBTK/ref_data/226.0```407 408This module sets `$GTDBTK_DATA_PATH` & `GTDBTK_DATA_ARCHIVED` environment variables pointing to the uncompressed and compressed reference data location.409 410### Usage with nf-core Pipelines411 412The GTDB-Tk r226 reference data is available for use with nf-core pipelines (e.g., nf-core/mag, nf-core/taxprofiler). Instead of downloading the ~100GB database, you simply specify the path to the pre-installed data.413 414The nf-core pipeline will use its own containerized version of the GTDB-Tk software and access your local reference data.415 416##### Example nf-core/mag pipeline417 418```bash419 420# Load bioinfo-user group modules421module load bioinfo-ugrp-modules422# Load the module to get database path423module load bioinfo/gtdbtk/r226-full424 425# Optional: set variables for output directory 426OUTDIR=/path/to/ouput/directory427 428# Run nf-core pipeline specifying the compressed database path429# Note: for uncompressed use GTDBTK_DATA_PATH430nextflow run nf-core/mag \431 --profile oist \432 --input samplesheet.csv \433 --outdir ${OUTDIR} \434 --gtdb_db ${GTDBTK_DATA_ARCHIVED} 435```436 437---438 439## Pfam440 441Version 34.0: Use `ml DB/Pfam/34.0` to invoke it in your scripts.442 443## Dfam444 445Version 3.9 downloaded from <https://www.dfam.org/releases/Dfam_3.9/families/> and <https://www.dfam.org/releases/Dfam_3.9/families/FamDB>. HDF5 files were uncompressed after checking their MD5 sums.446 447The command `ml DB/Dfam/3.9` exposes two environment variables448 - `$BioinfoUgrp_Dfam` containing the path to the directory containing the HMM files, that can be passed to RepeatMasker through its `-libdir` argument.449 - `$BioinfoUgrp_FamDB` containing the path to the directory containing the HDF5 files, to be bind-mounted on `/opt/RepeatMasker/Libraries/famdb/` when using `TETools`.450 - `SINGULARITY_BINDPATH`, with a value to replace `/opt/RepeatMasker/Libraries/famdb` in the Singularity containers with the local full copy of Dfam.451 452This is done with the following Lua module file.453 454```455-- Default settings456local modroot = ""/bucket/BioinfoUgrp""457local appname = myModuleName()458local appversion = myModuleVersion()459local apphome = pathJoin(modroot, myModuleFullName())460 461-- Package information462whatis(""Name: ""..appname)463whatis(""Version: ""..appversion)464whatis(""URL: ""..""https://dfam.org"")465whatis(""Category: ""..""bioinformatics"")466whatis(""Keywords: ""..""annotation, transposon, repeat"")467whatis(""Description: ""..""The Dfam open collection of Transposable Element DNA sequence alignments"")468 469-- Package settings470LmodMessage(""You can find the Dfam database HMMs in the directory pointed to\nby the environment variable $BioinfoUgrp_Dfam, and the\nHDF5 files in $BioinfoUgrp_FamDB."")471setenv(""BioinfoUgrp_Dfam"", apphome)472setenv(""BioinfoUgrp_FamDB"", apphome .. ""/FamDB"")473setenv(""SINGULARITY_BINDPATH"", apphome..""/FamDB:/opt/RepeatMasker/Libraries/famdb"")474```475 476## Dfam for RepeatMasker477 478The command `ml DB/Dfam_RepeatMasker/3.6__4.1.3` will set an environmental variable that changes the behaviour of the `repeatmodeler` module, so that it will use the full Dfam database provided by us instead of the “_curated only_” version provided by default.479 480### Developer details481 482The RepeatMasker program does not follow symbolic links and the Dfam database is large (160 Gb), so I had to use hard links to the files of the `Dfam` module instead. Also, the modulefile contains:483 484```485setenv(""BioinfoUgrp_Dfam_Rmsk_4_1_3"", apphome..""/RepeatMasker_4.1.3/Libraries"")486setenv(""SINGULARITY_BINDPATH"", apphome..""/Libraries:/opt/RepeatMasker/Libraries"")487```488","Markdown"
489"AlphaFold","oist/BioinfoUgrp","mkDebMedModule.sh",".sh","1711","63","#!/bin/bash -e490ml singularity491APP=$1492if [ -z ""$DEBVERSION"" ]493then494 printf 'Error: $DEBVERSION is not set and exported\n'495 exit 1496fi497 498printf ""==== $APP ====\n""499 500MODROOT=/bucket/BioinfoUgrp/DebianMed/$DEBVERSION501DEBMEDIMAGE=$MODROOT/DebianMed_$DEBVERSION.sif502APPDIR=$MODROOT/modules/$APP503VER=$(singularity exec $DEBMEDIMAGE dpkg-query -W -f='${Version}' $APP | perl -pe 's/^.*?://')504PROGLIST=$($DEBMEDIMAGE dpkg -L $APP | grep -v -e 'package diverts' -e 'diverted by' | grep /bin/) || true505if [ -z ""$PROGLIST"" ]506then507 printf ""Module not created: package $APP has no executables\n""508 exit 0509fi510 511printf "" creating module in $APPDIR/$VER\n""512 513mkdir -p $APPDIR/$VER/bin514cd $APPDIR/$VER515 516for prog in $(basename -a $PROGLIST)517do518cat <<__END__ > bin/$prog519#!/bin/sh520LC_ALL=C singularity exec $DEBMEDIMAGE $prog ""\$@"" 521__END__522chmod 775 bin/$prog523done524mkdir -p $MODROOT/modulefiles/$APP525cd $MODROOT/modulefiles/$APP526 527printf "" creating modulefile $VER in $MODROOT/modulefiles/$APP\n""528 529cat <<__END__ > $VER.lua530-- Default settings531local modroot = ""$MODROOT""532local appname = myModuleName()533local appversion = myModuleVersion()534local apphome = pathJoin(modroot, ""modules"", ""$APP"", appversion)535 536-- Package information537whatis(""Name: ""..appname)538whatis(""Version: ""..appversion)539whatis(""URL: ""..""https://github.com/oist/BioinfoUgrp"")540whatis(""Category: "".."" bioinformatics"")541whatis(""Keywords: "".."" Bioinformatics, Debian"")542whatis(""Description: "".."" Module automatically generated by the Bioinfo user group."")543 544help([[This module runs from Singularity image of Debian Med.545Please contact the Bioinfo user group for details.]])546 547-- Package settings548depends_on(""singularity"")549prepend_path(""PATH"", apphome..""/bin"")550__END__551","Shell"
552"AlphaFold","oist/BioinfoUgrp","RStudio/launch_rserver.sh",".sh","1801","57","#!/bin/sh -e553 554if [ ""$1"" = ""desktop"" ]; then555 # Replace the shell process with the rstudio process556 exec rstudio557fi558 559RSTUDIO_TEMP=$(mktemp -d -p ~)560trap ""{ rm -rf $RSTUDIO_TEMP; }"" EXIT561 562cat <<__DBCONF__ > $RSTUDIO_TEMP/dbconf563provider=sqlite564directory=$RSTUDIO_TEMP/db.sqlite3565__DBCONF__566 567 568export RSTUDIO_PASSWORD=${RSTUDIO_PASSWORD-`date -R | md5sum | cut -c-16`}569 570if [ -z ""$RSTUDIO_PORT"" ]571then572 # Taken from https://gitlab.oit.duke.edu/chsi-informatics/containers/singularity-rstudio-base/-/blob/master/port_and_password_1_3.sh573 LOWERPORT=50000574 UPPERPORT=65535575 for RSTUDIO_PORT in $(seq $LOWERPORT $UPPERPORT);576 do577 RSTUDIO_PORT=""`shuf -i $LOWERPORT-$UPPERPORT -n 1`""578 # echo ""Testing port: $RSTUDIO_PORT""579 ss -lpn | grep -q "":$RSTUDIO_PORT "" || break580 done581fi582 583RSTUDIO_HOST=$(hostname -A | cut -f1 -d' ')584RSTUDIO_HOST=${RSTUDIO_HOST:-localhost}585 586printf ""\nRStudio URL:\t\thttp://${RSTUDIO_HOST}:${RSTUDIO_PORT}/\n""587printf ""RStudio Username:\t$USER\n""588printf ""RStudio Password:\t$RSTUDIO_PASSWORD\n""589if [ ! $RSTUDIO_HOST = ""localhost"" ]590then591 printf ""\nIf you remote work, you can forward the server to port 1664 on your computer with:\n""592 printf ""ssh ${USER}@${RSTUDIO_HOST} -J ${USER}@login.oist.jp,${USER}@deigo.oist.jp -L 1664:localhost:${RSTUDIO_PORT}\n""593fi594printf ""\nYou may need to clean your temporary files by yourself:\n""595printf ""RStudio temporary files:\t$RSTUDIO_TEMP\n""596printf ""\nThis image will build its packages in the following directory if it exists:\n""597grep ^R_LIBS_USER /etc/R/Renviron.site598printf ""\n""599 600/usr/lib/rstudio-server/bin/rserver \601 --server-working-dir $RSTUDIO_TEMP \602 --server-data-dir $RSTUDIO_TEMP \603 --database-config-file $RSTUDIO_TEMP/dbconf \604 --server-user=$USER \605 --www-port=$RSTUDIO_PORT \606 --auth-none 0 \607 --auth-pam-helper rstudio_auth608","Shell"
609"AlphaFold","oist/BioinfoUgrp","RStudio/rstudio_auth.sh",".sh","569","28","#!/usr/bin/env bash610 611# Confirm username is supplied612if [[ $# -lt 1 ]]; then613 echo ""Usage: auth USERNAME""614 exit 1615fi616USERNAME=""${1}""617 618# Confirm password environment variable exists619if [[ -z ""${RSTUDIO_PASSWORD}"" ]]; then620 echo ""The environment variable RSTUDIO_PASSWORD is not set""621 exit 1622fi623 624# Read in the password from user625read -s -p ""Password: "" PASSWORD626echo """"627 628# Authenticate user629if [[ ""${USER}"" == ""${USERNAME}"" && ""${PASSWORD}"" == ""${RSTUDIO_PASSWORD}"" ]]; then630 echo ""Successful authentication""631 exit 0632else633 echo ""Invalid authentication""634 exit 1635fi636","Shell"
637"AlphaFold","oist/BioinfoUgrp","AlphaFold/AlphaFold2.md",".md","6034","106","# Alphafold 2.0 and 2.1 @ SAION638 639*Disclaimer: this implementation was made for general use with the help of Jan Moren of SCS. I do take no responsibility for bugs or errors, but if you could report them, I will gladly try to fix on my extra time. Nonetheless, the AF2 predictions appear to be working. Feel free but not obligated to acknowledge me or at least the SCS if this work was helpful for your research.*640 641In order to use AF2, you need [SAION access](https://oist.service-now.com/sp?id=sc_category&sys_id=9c71871fdbcdeb806885f00ebf961928) and have basic knowledge of the [terminal](https://groups.oist.jp/scs/basic-linux-commands) and [slurm submission commands](https://groups.oist.jp/scs/use-slurm). 642AF2 is part of the OIST [Bioinfo User group](https://github.com/oist/BioinfoUgrp). 643AF2 was implemented using the [docker image](https://hub.docker.com/r/uvarc/alphafold) made by the University of Virginia, that here we gratefully acknowledge.644## AF2 content645### AF 2.0646* 'alphafold_2.0.0.sif': singularity image created from the previously mentioned docker file647* 'run_alphafold.sh': AF2 run script. Contains the default parameters (except input file and output folder). DO NOT MODIFY648* 'alphafold_example_script.sh': AF2 sbatch example. Copy to your folder and modify (add input file and output folder paths).649* 'get_plddt_attribfile.py': Chimera attribute file generator. Automatically generates an attribute file for plddt coloring in chimera.650### AF 2.1651* 'alphafold_2.1.1.sif': singularity image created from the previously mentioned docker file652* 'run_alphafold.sh': AF2 run script. Contains the default parameters (except input file and output folder). DO NOT MODIFY653* 'run_alphafold_multimer.sh': AF2 run script specialized in multimer run. Contains the default parameters (except input file and output folder). DO NOT MODIFY654* 'alphafold_example_script.sh': AF2 sbatch example. Copy to your folder and modify (add input file and output folder paths).655* 'get_plddt_attribfile.py': Chimera attribute file generator. Automatically generates an attribute file for plddt coloring in chimera.656 657MULTIMER RUN [instructions](https://github.com/deepmind/alphafold#running-alphafold-multimer)658TL;DR: provide a multi fasta file as input.659 660## Example run661Assume to have a folder in /work with the input single protein sequence: example.fasta and a test output folder: test_out/. 662Copy the example script:663> cp /bucket/BioinfoUgrp/alphafold/2.1.1/bin/alphafold_example_script.sh .664 665Change the file name and modify the input and output folder paths, using your favourite text editor: 666 667> mv alphafold_example_script.sh AF2_testrun.sh 668> vim AF2_testrun.sh 669> (change input file and output folder, save and exit) 670 671OPTIONAL: CHECK IF THE RESOURCES YOU ARE REQUESTING VIA SLURM ARE ENOUGH (by default 4cpu cores, 100GB, 1 GPU) 672 673Submit the job: 674 675> sbatch AF2_testrun.sh 676 677The job is expected to take 2 to 12+ hours depending on sequence lenght.678 679## Output680A description of the output can be found in [AlphaFold 2 Github page](https://github.com/deepmind/alphafold/blob/main/README.md#alphafold-output). 681However, for lazy people, ranked_0.pdb is the highest scoring model.682 683## Example script684For convenience, we report here the example script content for version 2.1.1. 685 686> #!/bin/bash 687> #SBATCH --job-name=test_af 688> #SBATCH -c 4 689> #SBATCH --mem=100G 690> #SBATCH --partition=gpu 691> #SBATCH -t 4-0 692> #SBATCH --gres=gpu:1 693> 694> module load bioinfo-ugrp-modules 695> module load alphafold/2.1.1 696> 697> \# Uncomment the monomer or multimer depending on the use case 698> \# Monomer 699> \# run_alphafold.sh --fasta_paths test.fa --output_dir test_output 700> \# Multimer 701> \# run_alphafold_multimer.sh --fasta_paths multifasta_test.fa --output_dir test_output 702 703 704## Attrib file705If you use Chimera to visualize the pdb file, you might be interested in per-residue plddt coloring. plddt is the self-evaluated confidence measure of the prediction of alphafold2. It goes from 0 (low confidence) to 100 (high confidence). A low value indicates either badly predicted regions or disordered regions. 706To automatically generate a chimera attribute file for coloring by plddt, you can use the python script I made:707> module load python/3.7.3 708> python /bucket/BioinfoUgrp/alphafold/2.0.0/bin/get_plddt_attribfile.py <result_model_X.pkl> <outfile.txt>709The text file generated can be used in Chimera (Tools > Structure Analysis > Define Attribute) after opening the same pdb model. 710 711## Appendix: parameters712This is a list of all the default parameters in the run_alphafold script. If you want to modify them, do not change the default script. Instead, provide them to the example run script just like the input fasta and output folder. 713Default parameters (v2.0):714> MAX_TEMPLATE_DATE=2030-09-09 715> MODEL_NAMES=model_1,model_2,model_3,model_4,model_5 716> DATA_DIR=/bucket/BioinfoUgrp/alphafold/database/717> UNIREF90_PATH=$DATA_DIR/uniref90/uniref90.fasta 718> MGNIFY_PATH=$DATA_DIR/mgnify/mgy_clusters.fa 719> UNICLUST30_PATH=$DATA_DIR/uniclust30/uniclust30_2018_08/uniclust30_2018_08 720> BFD_PATH=$DATA_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt 721> PDB70_PATH=$DATA_DIR/pdb70/pdb70 722> TEMPLATE_PATH=$DATA_DIR/pdb_mmcif/mmcif_files/ 723> OBSOLETE_PATH=$DATA_DIR/pdb_mmcif/obsolete.dat 724 725Default parameters (v2.1):726> MAX_TEMPLATE_DATE=2030-09-09 727> MODEL_PRESET=multimer 728> DATA_DIR=/bucket/BioinfoUgrp/alphafold/database/729> UNIREF90_PATH=$DATA_DIR/uniref90/uniref90.fasta 730> MGNIFY_PATH=$DATA_DIR/mgnify/mgy_clusters.fa 731> UNICLUST30_PATH=$DATA_DIR/uniclust30/uniclust30_2018_08/uniclust30_2018_08 732> BFD_PATH=$DATA_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt 733> PDB70_PATH=$DATA_DIR/pdb70/pdb70 734> TEMPLATE_PATH=$DATA_DIR/pdb_mmcif/mmcif_files/ 735> OBSOLETE_PATH=$DATA_DIR/pdb_mmcif/obsolete.dat 736> PDB_SEQRES_PATH=$DATA_DIR/pdb_seqres/pdb_seqres.txt 737> UNIPROT_PATH=$DATA_DIR/uniprot/ 738 739 740## Appendix: contact741Stefano Pascarelli, PhD, Laurino unit742","Markdown"
743"AlphaFold","oist/BioinfoUgrp","Other/Assembly.md",".md","16928","630","# Bioinformatics modules for genome assembly744 745To use the modules, load the `bioinfo-ugrp-modules` metamodule first.746 747```bash748ml bioinfo-ugrp-modules749ml av Other750ml Other/<your-favorite-module>751```752 753## assembly-stats754 755- Home page: https://github.com/sanger-pathogens/assembly-stats756- Source code: https://github.com/sanger-pathogens/assembly-stats757 758### Installation on Deigo759 760```bash761APP=assembly-stats762VER=1.0.1763MODROOT=/bucket/BioinfoUgrp/Other764APPDIR=$MODROOT/$APP765mkdir -p $APPDIR766cd $APPDIR767wget -O - https://github.com/sanger-pathogens/assembly-stats/archive/refs/tags/v1.0.1.tar.gz | tar xzvf -768mv $APP-$VER $VER769cd $VER && mkdir build && cd build770cmake -DINSTALL_DIR:PATH=$APPDIR/$VER ..771make test772make install773cd $MODROOT/modulefiles/774mkdir -p $APP775cat <<'__END__' > $APP/$VER.lua776-- Default settings777local modroot = ""/bucket/BioinfoUgrp""778local appname = myModuleName()779local appversion = myModuleVersion()780local apphome = pathJoin(modroot, myModuleFullName())781 782-- Package information783whatis(""Name: ""..appname)784whatis(""Version: ""..appversion)785whatis(""URL: ""..""https://github.com/sanger-pathogens/assembly-stats"")786whatis(""Category: ""..""bioinformatics"")787whatis(""Keywords: ""..""assembly-stats"")788whatis(""Description: ""..""Get assembly statistics from FASTA and FASTQ files."")789 790-- Package settings791prepend_path(""PATH"", apphome)792__END__793```794 795### Example commands for running assembly-stats on Deigo796 797```bash798ml Other/assembly-stats799srun -p compute -c 1 --mem 10G -t 00:10:00 --pty \800 assembly-stats contigs.fasta801```802 803## BandageNG804 805- Home page: https://github.com/asl/BandageNG806- Source code: https://github.com/asl/BandageNG807 808### Installation on Deigo809 810I created a Singularity image with the following definition file on my Linux laptop.811 812```813Bootstrap: docker814From: debian:bookworm815 816 817%runscript818 exec /squashfs-root/AppRun ""$@""819 820%post821 # Update the image822 apt update823 apt upgrade -y824 825 # Add a package needed to suppress some debconf error messages826 apt install -y whiptail827 828 # Install all locales829 apt install -y locales-all830 831 # Install FUSE to extract and run the AppImage832 apt install -y fuse3833 # X11 and other dependencies834 apt install -y x11-apps mesa-utils libgl1 libglu1-mesa835 apt install -y dbus836 dbus-uuidgen > /etc/machine-id837 838 # Download BandageNG839 apt install -y wget840 wget https://github.com/asl/BandageNG/releases/download/continuous/BandageNG-Linux-827c5cb.AppImage841 chmod 775 BandageNG-Linux-827c5cb.AppImage842 ./BandageNG-Linux-827c5cb.AppImage --appimage-extract843 844 # Clean downoladed package cache. Yes I know about /var/libs.845 apt clean846```847 848Then, I copied it in my home directory on _deigo_.849 850```bash851APP=BandageNG852VER=2025-03-28853MODROOT=/bucket/BioinfoUgrp/Other854APPDIR=$MODROOT/$APP855mkdir -p $APPDIR/$VER856cd $APPDIR/$VER857cp ~/BandageNG.sif BandageNG858cd $MODROOT/modulefiles/859mkdir -p $APP860cat <<'__END__' > $APP/$VER.lua861-- Default settings862local modroot = ""/bucket/BioinfoUgrp""863local appname = myModuleName()864local appversion = myModuleVersion()865local apphome = pathJoin(modroot, myModuleFullName())866 867-- Package information868whatis(""Name: ""..appname)869whatis(""Version: ""..appversion)870whatis(""URL: ""..""https://github.com/chaoszhang/ASTER"")871whatis(""Category: ""..""bioinformatics"")872whatis(""Keywords: ""..""BandageNG"")873whatis(""Description: "".."" a Bioinformatics Application for Navigating De novo Assembly Graphs Easily"")874 875-- Package settings876depends_on(""singularity"")877prepend_path(""PATH"", apphome)878__END__879```880 881## pbgzip882 883- Home page: https://github.com/nh13/pbgzip884- Source code: https://github.com/nh13/pbgzip885 886### Installation on Deigo887 888```bash889APP=pbgzip890VER=20160804891MODROOT=/bucket/BioinfoUgrp/Other892APPDIR=$MODROOT/$APP893mkdir -p $APPDIR894cd $APPDIR895git clone https://github.com/nh13/pbgzip896mv pbgzip $VER && cd $VER 897sh autogen.sh && ./configure --prefix=$APPDIR/$VER && make 898make install899cd $MODROOT/modulefiles/900mkdir -p $APP901cat <<'__END__' > $APP/$VER.lua902-- Default settings903local modroot = ""/bucket/BioinfoUgrp""904local appname = myModuleName()905local appversion = myModuleVersion()906local apphome = pathJoin(modroot, myModuleFullName())907 908-- Package information909whatis(""Name: ""..appname)910whatis(""Version: ""..appversion)911whatis(""URL: ""..""https://github.com/nh13/pbgzip"")912whatis(""Category: ""..""bioinformatics"")913whatis(""Keywords: ""..""pbgzip"")914whatis(""Description: ""..""This tool and API implements parallel block gzip."")915 916-- Package settings917prepend_path(""PATH"", apphome)918__END__919```920 921### Example commands for running pbgzip on Deigo922 923```bash924module load Other/pbgzip925srun -p compute -c 128 --mem 100G -t 1:00:00 --pty \926 pbgzip <arguments>927```928 929## SMARTdenovo930 931```bash932APP=SMARTdenovo933VER=2021-02-24934MODROOT=/bucket/BioinfoUgrp/Other935APPDIR=$MODROOT/$APP/$VER936mkdir -p $MODROOT/$APP937cd $MODROOT/$APP938git clone https://github.com/ruanjue/smartdenovo $VER939ml gcc940cd $VER941make942cd $MODROOT/modulefiles/943mkdir -p $APP944cat <<'__END__' > $APP/$VER.lua945-- Default settings946local modroot = ""/bucket/BioinfoUgrp""947local appname = myModuleName()948local appversion = myModuleVersion()949local apphome = pathJoin(modroot, myModuleFullName())950 951-- Package information952whatis(""Name: ""..appname)953whatis(""Version: ""..appversion)954whatis(""URL: ""..""https://github.com/ruanjue/smartdenovo"")955whatis(""Category: ""..""bioinformatics"")956whatis(""Keywords: ""..""PacBio, Nanopore, genome, assembler"")957whatis(""Description: ""..""de novo assembler for PacBio and Oxford Nanopore (ONT) data"")958 959-- Package settings960prepend_path(""PATH"", apphome)961__END__962```963 964## BUSCO965 966- Home page: https://busco.ezlab.org/967- Source code: https://gitlab.com/ezlab/busco968 969### Installation on Deigo970 971```bash972module load singularity973APP=BUSCO974VER=5.8.2975MODROOT=/bucket/BioinfoUgrp/Other976APPDIR=$MODROOT/$APP/$VER977mkdir -p $APPDIR978cd $APPDIR979singularity pull busco.sif docker://ezlabgva/busco:v${VER}_cv1980echo '#!/bin/sh' > busco && echo ""singularity exec $APPDIR/busco.sif busco \$*"" >> busco && chmod +x busco981cd $MODROOT/modulefiles/982mkdir -p $APP983cat <<'__END__' > $APP/$VER.lua984-- Default settings985local modroot = ""/bucket/BioinfoUgrp""986local appname = myModuleName()987local appversion = myModuleVersion()988local apphome = pathJoin(modroot, myModuleFullName())989 990-- Package information991whatis(""Name: ""..appname)992whatis(""Version: ""..appversion)993whatis(""URL: ""..""https://busco.ezlab.org/"")994whatis(""Category: ""..""bioinformatics"")995whatis(""Keywords: ""..""assembly"")996whatis(""Description: ""..""Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)."")997 998-- Package settings999depends_on(""singularity"")1000prepend_path(""PATH"", apphome)1001 1002LmodMessage([[1003================================================================================1004The BUSCO module runs a read-only Singularity image.1005 1006If you need to change AUGUSTUS configuration, you can do a local copy with the1007following command that will place it in $HOME/augustus_config.1008 1009 singularity exec /bucket/BioinfoUgrp/Other/BUSCO/5.8.2/busco.sif cp -r /usr/local/config $HOME/augustus_config1010 1011You can then pass the information by exporting the AUGUSTUS_CONFIG_PATH variable.1012 1013 export AUGUSTUS_CONFIG_PATH=""$HOME/augustus_config""1014================================================================================1015]])1016__END__1017```1018 1019### Example commands for running BUSCO on Deigo1020 1021The following command executes `$ busco` using the Singularity image:1022 1023```bash1024module load Other/BUSCO1025srun -p compute -c 128 --mem 500G -t 24:00:00 --pty \1026 busco.sif <arguments> 1027```1028 1029We also provide a command `busco` that is effectively the same as above:1030 1031```bash1032module load Other/BUSCO1033srun -p compute -c 128 --mem 500G -t 24:00:00 --pty \1034 busco <arguments>1035```1036 1037**IMPORTANT: Using Augustus for BUSCO running via its Singularity image requires the Augustus' config directory to be copied (from inside of Singularity container environment) to your own environment (outside Singularity in Deigo). The module we provide automatically copy the config directory to `$HOME/augustus_config` if it does not exist yet, and also set the `AUGUSTUS_CONFIG_PATH` varieble as `$HOME/augustus_config`, when the module is loaded.**1038 1039## gfatools1040 1041- Home page: https://github.com/lh3/gfatools1042- Source code: https://github.com/lh3/gfatools/releases1043 1044### Installation on Deigo1045 1046```bash1047APP=gfatools1048VER=0.51049MODROOT=/bucket/BioinfoUgrp/Other1050APPDIR=$MODROOT/$APP1051mkdir -p $APPDIR1052cd $APPDIR1053wget -O - https://github.com/lh3/gfatools/archive/refs/tags/v$VER.tar.gz | tar xzvf -1054mv $APP-$VER $VER1055cd $VER && make1056cd $MODROOT/modulefiles/1057mkdir -p $APP1058cat <<'__END__' > $APP/$VER.lua1059-- Default settings1060local modroot = ""/bucket/BioinfoUgrp""1061local appname = myModuleName()1062local appversion = myModuleVersion()1063local apphome = pathJoin(modroot, myModuleFullName())1064 1065-- Package information1066whatis(""Name: ""..appname)1067whatis(""Version: ""..appversion)1068whatis(""URL: ""..""https://github.com/lh3/gfatools"")1069whatis(""Category: ""..""bioinformatics"")1070whatis(""Keywords: ""..""gfa, assembly"")1071whatis(""Description: ""..""Tools for manipulating sequence graphs in the GFA and rGFA formats."")1072 1073-- Package settings1074prepend_path(""PATH"", apphome)1075__END__1076```1077 1078### Example commands for running gfatools on Deigo1079 1080```bash1081module load Other/gfatools1082srun -p compute -c 1 --mem 40G -t 1:00:00 --pty \1083 gfatools <arguments>1084```1085 1086## hifiasm1087 1088- Home page: https://github.com/chhylp123/hifiasm1089- Source code: https://github.com/chhylp123/hifiasm/releases1090 1091### Installation on Deigo1092 1093```bash1094APP=hifiasm1095VER=0.25.01096MODROOT=/bucket/BioinfoUgrp/Other1097APPDIR=$MODROOT/$APP1098mkdir -p $APPDIR1099cd $APPDIR1100wget -O - https://github.com/chhylp123/hifiasm/archive/refs/tags/$VER.tar.gz | tar xzvf -1101mv $APP-$VER $VER1102cd $VER1103ml purge && ml gcc/11.2.11104make CXXFLAGS=""-g -O3 -mavx2 -mpopcnt -fomit-frame-pointer -Wall"" # Replace SSE with AVX. When updating, check that the other flags did not change.1105cd /bucket/BioinfoUgrp/Other/modulefiles/hifiasm1106cp 0.20.0.lua ${VER}.lua1107```1108 1109### Example commands for running hifiasm on Deigo1110 1111```bash1112module load Other/hifiasm1113srun -p compute -c 64 --mem 500G -t 24:00:00 --pty \1114 hifiasm <arguments>1115```1116 1117## Canu (and HiCanu)1118 1119- Home page: https://github.com/marbl/canu1120- Source code: https://github.com/marbl/canu/releases1121 1122### Installation on Deigo1123 1124```bash1125APP=canu1126VER=2.31127MODROOT=/bucket/BioinfoUgrp/Other1128APPDIR=$MODROOT/$APP1129mkdir -p $APPDIR1130cd $APPDIR1131wget -O - https://github.com/marbl/canu/releases/download/v$VER/$APP-$VER.Linux-amd64.tar.xz | tar Jxvf -1132mv $APP-$VER $VER1133cd $MODROOT/modulefiles/1134mkdir -p $APP1135cat <<'__END__' > $APP/$VER.lua1136-- Default settings1137local modroot = ""/bucket/BioinfoUgrp""1138local appname = myModuleName()1139local appversion = myModuleVersion()1140local apphome = pathJoin(modroot, myModuleFullName())1141 1142-- Package information1143whatis(""Name: ""..appname)1144whatis(""Version: ""..appversion)1145whatis(""URL: ""..""https://github.com/marbl/canu"")1146whatis(""Category: ""..""bioinformatics"")1147whatis(""Keywords: ""..""assembly"")1148whatis(""Description: ""..""A single molecule sequence assembler for genomes large and small."")1149 1150-- Package settings1151depends_on(""samtools"")1152prepend_path(""PATH"", apphome..""/bin"")1153__END__1154```1155 1156### Example commands for running Canu on Deigo1157 1158```bash1159module load Other/canu1160srun -p compute -c 128 --mem 500G -t 24:00:00 --pty \1161 canu <arguments>1162```1163 1164## purge_dups1165 1166- Home page: https://github.com/dfguan/purge_dups1167- Source code: https://github.com/dfguan/purge_dups1168 1169### Installation on Deigo1170 1171**WARNING: This module currently does not support the optional runner script nor k-mer comparision plot.**1172 1173```bash1174APP=purge_dups1175VER=1.2.51176MODROOT=/bucket/BioinfoUgrp/Other1177APPDIR=$MODROOT/$APP1178mkdir -p $APPDIR1179cd $APPDIR1180git clone https://github.com/dfguan/purge_dups1181mv purge_dups $VER && cd $VER/src && make1182cd $MODROOT/modulefiles/1183mkdir -p $APP1184cat <<'__END__' > $APP/$VER.lua1185-- Default settings1186local modroot = ""/bucket/BioinfoUgrp""1187local appname = myModuleName()1188local appversion = myModuleVersion()1189local apphome = pathJoin(modroot, myModuleFullName())1190 1191-- Package information1192whatis(""Name: ""..appname)1193whatis(""Version: ""..appversion)1194whatis(""URL: ""..""https://github.com/dfguan/purge_dups"")1195whatis(""Category: ""..""bioinformatics"")1196whatis(""Keywords: ""..""assembly"")1197whatis(""Description: ""..""haplotypic duplication identification tool."")1198 1199-- Package settings1200depends_on(""Other/minimap2"")