Commit eed677aa authored by Eric CHARPENTIER's avatar Eric CHARPENTIER 🐍
Browse files

added tools versions in report, cleaned scripts

parent b27c68ac
#!/bin/bash
# creation d'environnements conda specifiques au pipeline
echo $PATH
echo "=== create conda environments ==="
echo "=== deseq2 ==="
conda create -yq -n deseq2 bioconductor-deseq2 bioconductor-biomart xorg-libxrender xorg-libxext xorg-libsm --override-channels -c conda-forge -c bioconda
echo "=== rnaSeqQuantif ==="
conda create -yq -n rnaSeqQuantif snakemake perl openjdk fastqc multiqc cutadapt prinseq star htseq gzip ncurses --override-channels -c bioconda -c conda-forge -c ostrokach
name: deseq2
channels:
- dougal
- r
- bird
- conda-forge
- bioconda
- defaults
dependencies:
- bioconductor-annotate=1.56.0=r3.4.1_0
- bioconductor-annotationdbi=1.40.0=r3.4.1_0
- bioconductor-biobase=2.38.0=r3.4.1_0
- bioconductor-biocgenerics=0.24.0=r3.4.1_0
- bioconductor-biocparallel=1.12.0=r3.4.1_0
- bioconductor-biomart=2.34.2=r3.4.1_0
- bioconductor-delayedarray=0.4.1=r3.4.1_0
- bioconductor-deseq2=1.18.1=r3.4.1_1
- bioconductor-genefilter=1.60.0=r3.4.1_0
- bioconductor-geneplotter=1.56.0=r3.4.1_0
- bioconductor-genomeinfodb=1.14.0=r3.4.1_0
- bioconductor-genomeinfodbdata=1.0.0=r3.4.1_1
- bioconductor-genomicranges=1.30.3=r3.4.1_0
- bioconductor-iranges=2.12.0=r3.4.1_0
- bioconductor-s4vectors=0.16.0=r3.4.1_0
- bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
- bioconductor-tximport=1.6.0=r3.4.1_0
- bioconductor-xvector=0.18.0=r3.4.1_0
- bioconductor-zlibbioc=1.24.0=r3.4.1_0
- bzip2=1.0.6=h470a237_2
- ca-certificates=2018.4.16=0
- cairo=1.14.12=he56eebe_1
- curl=7.60.0=0
- fontconfig=2.13.0=h074f895_2
- freetype=2.8.1=0
- gettext=0.19.8.1=0
- glib=2.55.0=0
- graphite2=1.3.11=hfc679d8_0
- gsl=2.1=2
- harfbuzz=1.7.6=0
- icu=58.2=hfc679d8_0
- jpeg=9c=h470a237_0
- krb5=1.14.6=0
- libffi=3.2.1=3
- libiconv=1.15=h470a237_1
- libpng=1.6.34=ha92aebf_1
- libssh2=1.8.0=h5b517e9_2
- libtiff=4.0.9=he6b73bb_1
- libuuid=1.0.3=1
- libxcb=1.13=h470a237_1
- libxml2=2.9.8=h422b904_2
- ncurses=5.9=10
- openssl=1.0.2o=0
- pango=1.40.14=hd50be51_1
- pcre=8.39=0
- pixman=0.34.0=2
- pthread-stubs=0.4=h470a237_1
- r-acepack=1.4.1=r3.4.1_0
- r-assertthat=0.2.0=r3.4.1_0
- r-backports=1.1.2=r3.4.1_0
- r-base=3.4.1=4
- r-base64enc=0.1_3=r3.4.1_0
- r-bh=1.66.0_1=r3.4.1_0
- r-bit=1.1_12=r3.4.1_0
- r-bit64=0.9_5=r3.4.1_0
- r-bitops=1.0_6=r3.4.1_0
- r-blob=1.1.1=r3.4.1_0
- r-catools=1.17.1=r3.4.1_0
- r-checkmate=1.8.5=r3.4.1_0
- r-cli=1.0.0=r3.4.1_0
- r-cluster=2.0.6=r3.4.1_0
- r-colorspace=1.3_2=r3.4.1_0
- r-crayon=1.3.4=r3.4.1_0
- r-curl=3.2=r3.4.1_0
- r-data.table=1.11.4=r341hc070d10_0
- r-dbi=1.0.0=r341_0
- r-dichromat=2.0_0=r3.4.1_0
- r-digest=0.6.15=r3.4.1_0
- r-evaluate=0.10.1=r3.4.1_0
- r-foreign=0.8_67=r3.4.1_0
- r-formula=1.2_1=r3.4.1_0
- r-futile.logger=1.4.3=r3.4.1_0
- r-futile.options=1.0.0=r3.4.1_0
- r-gdata=2.18.0=r3.4.1_0
- r-getopt=1.20.2=r3.4.1_0
- r-ggplot2=3.0.0=r341h6115d3f_0
- r-glue=1.2.0=r3.4.1_0
- r-gplots=3.0.1=r3.4.1_0
- r-gridextra=2.3=r3.4.1_0
- r-gtable=0.2.0=r3.4.1_0
- r-gtools=3.8.1=r341_0
- r-highr=0.7=r341_0
- r-hmisc=4.0_3=r3.4.1_0
- r-hms=0.3=r3.4.1_0
- r-htmltable=1.9=r3.4.1_0
- r-htmltools=0.3.6=r3.4.1_0
- r-htmlwidgets=1.0=r3.4.1_0
- r-httr=1.3.1=r3.4.1_0
- r-jsonlite=1.5=r3.4.1_0
- r-kernsmooth=2.23_15=r3.4.1_0
- r-knitr=1.20=r3.4.1_0
- r-labeling=0.3=r3.4.1_0
- r-lambda.r=1.2=r3.4.1_0
- r-lattice=0.20_34=r3.4.1_0
- r-latticeextra=0.6_28=r3.4.1_0
- r-lazyeval=0.2.1=r3.4.1_0
- r-locfit=1.5_9.1=r3.4.1_0
- r-magrittr=1.5=r3.4.1_0
- r-markdown=0.8=r3.4.1_1
- r-mass=7.3_50=r341hc070d10_0
- r-matrix=1.2_14=r3.4.1_0
- r-matrixstats=0.53.1=r341_0
- r-memoise=1.1.0=r3.4.1_0
- r-mgcv=1.8_24=r341_0
- r-mime=0.5=r3.4.1_0
- r-munsell=0.5.0=r341_0
- r-nlme=3.1_131=r3.4.1_0
- r-nnet=7.3_12=r3.4.1_0
- r-openssl=1.0.1=r3.4.1_0
- r-pillar=1.2.2=r341h6115d3f_1
- r-pkgconfig=2.0.1=r3.4.1_0
- r-plogr=0.2.0=r341h6115d3f_0
- r-plyr=1.8.4=r3.4.1_0
- r-prettyunits=1.0.2=r3.4.1_0
- r-progress=1.2.0=r341_0
- r-r6=2.2.2=r3.4.1_0
- r-rcolorbrewer=1.1_2=r3.4.1_0
- r-rcpp=0.12.17=r341h9d2a408_0
- r-rcpparmadillo=0.8.500.0=r3.4.1_0
- r-rcurl=1.95_4.11=r341ha4d7672_0
- r-reshape2=1.4.3=r3.4.1_0
- r-rjson=0.2.15=r3.4.1_0
- r-rlang=0.2.1=r341_0
- r-rpart=4.1_13=r3.4.1_0
- r-rsqlite=2.0=r3.4.1_0
- r-scales=0.5.0=r3.4.1_0
- r-snow=0.4_2=r3.4.1_0
- r-stringi=1.2.3=r341_0
- r-stringr=1.3.1=r341_0
- r-survival=2.42_6=r341_0
- r-tibble=1.4.2=r3.4.1_0
- r-utf8=1.1.3=r3.4.1_0
- r-viridis=0.5.1=r3.4.1_0
- r-viridislite=0.3.0=r3.4.1_0
- r-withr=2.1.1=r3.4.1_0
- r-xml=3.98_1.11=r341_0
- r-xtable=1.8_2=r3.4.1_0
- r-yaml=2.1.19=r341_0
- readline=7.0=0
- tk=8.6.7=0
- xorg-kbproto=1.0.7=h470a237_2
- xorg-libice=1.0.9=h470a237_3
- xorg-libsm=1.2.2=h470a237_3
- xorg-libx11=1.6.5=h470a237_1
- xorg-libxau=1.0.8=h470a237_5
- xorg-libxdmcp=1.1.2=h470a237_6
- xorg-libxext=1.3.3=h470a237_3
- xorg-libxrender=0.9.10=h470a237_1
- xorg-renderproto=0.11.1=h470a237_2
- xorg-xextproto=7.3.0=h470a237_2
- xorg-xproto=7.0.31=h470a237_7
- xz=5.2.3=0
- zlib=1.2.11=h470a237_3
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=7.2.0=hdf63c60_3
- libstdcxx-ng=7.2.0=hdf63c60_3
- wget=1.19.5=h1ad7b7a_0
prefix: /home/vintache-d/miniconda3/envs/deseq2
name: fastqc
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- fastqc=0.11.7=4
- libgcc-ng=7.2.0=hdf63c60_3
- openjdk=8.0.144=zulu8.23.0.3_2
- perl=5.26.2=h470a237_0
prefix: /home/vintache-d/RNAseq_quantif_pipeline/miniconda/envs/fastqc
name: dgeDE
channels:
- conda-forge
- defaults
dependencies:
- bzip2=1.0.6=h470a237_2
- ca-certificates=2018.10.15=ha4d7672_0
- cairo=1.14.12=h276e583_5
- curl=7.61.0=h93b3f91_2
- expat=2.2.5=hfc679d8_2
- fontconfig=2.13.1=h65d0f4c_0
- freetype=2.9.1=h6debe1e_4
- gettext=0.19.8.1=h5e8e0c9_1
- glib=2.56.2=h464dc38_0
- graphite2=1.3.12=hfc679d8_1
- harfbuzz=1.9.0=hee26f79_1
- icu=58.2=hfc679d8_0
- jpeg=9c=h470a237_1
- krb5=1.14.6=0
- libffi=3.2.1=hfc679d8_5
- libgcc-ng=7.2.0=hdf63c60_3
- libgfortran=3.0.0=1
- libiconv=1.15=h470a237_3
- libpng=1.6.35=ha92aebf_2
- libssh2=1.8.0
- libstdcxx-ng=7.2.0=hdf63c60_3
- libtiff=4.0.9=he6b73bb_2
- libuuid=2.32.1=h470a237_2
- libxcb=1.13=h470a237_2
- libxml2=2.9.8=h422b904_5
- ncurses=6.1=hfc679d8_1
- openssl=1.0.2p=h470a237_1
- pango=1.40.14=he752989_2
- pcre=8.41=hfc679d8_3
- pixman=0.34.0=h470a237_3
- pthread-stubs=0.4=h470a237_1
- r-base
- r-xml
- readline=7.0=haf1bffa_1
- tk=8.6.8=ha92aebf_0
- xorg-kbproto=1.0.7=h470a237_2
- xorg-libice=1.0.9=h470a237_4
- xorg-libsm=1.2.2=h8c8a85c_6
- xorg-libx11=1.6.6=h470a237_0
- xorg-libxau=1.0.8=h470a237_6
- xorg-libxdmcp=1.1.2=h470a237_7
- xorg-libxext=1.3.3=h470a237_4
- xorg-libxrender=0.9.10=h470a237_2
- xorg-libxt=1.1.5=h470a237_2
- xorg-renderproto=0.11.1=h470a237_2
- xorg-xextproto=7.3.0=h470a237_2
- xorg-xproto=7.0.31=h470a237_7
- xz=5.2.4=h470a237_1
- zlib=1.2.11=h470a237_3
- gsl=2.2.1=h0c605f7_3
- udunits2=2.2.25=hd30922c_1
name: rnaSeqQuantif
channels:
- ostrokach
- conda-forge
- bioconda
- defaults
dependencies:
- bcftools=1.9=h4da6232_0
- cutadapt=1.16=py36_2
- filechunkio=1.6=py36_0
- ftputil=3.2=py36_0
- htseq=0.9.1=py36h24bf2e0_1
- htslib=1.7=0
- libdeflate=1.0=h470a237_0
- multiqc=1.6=py36h24bf2e0_0
- perl-threaded=5.22.0=13
- prinseq=0.20.4=2
- pyasn1-modules=0.0.5=py36_0
- pysam=0.14.1=py36hae42fb6_1
- pysftp=0.2.9=py36_0
- rsa=3.1.4=py36_0
- samtools=1.7=1
- simplejson=3.8.1=py36_0
- snakemake=4.6.0=py36_0
- star=2.6.1a=1
- urllib3=1.12=py36_0
- xopen=0.3.2=py36_0
- aioeasywebdav=2.2.0=py36_0
- aiohttp=3.3.2=py36h470a237_1
- appdirs=1.4.3=py_1
- asn1crypto=0.24.0=py36_2
- async-timeout=3.0.0=py36_0
- attrs=18.1.0=py_1
- blas=1.1=openblas
- boto3=1.7.80=py_0
- botocore=1.10.80=py_0
- bzip2=1.0.6=h470a237_2
- ca-certificates=2018.8.13=ha4d7672_0
- cachetools=2.1.0=py_0
- certifi=2018.8.13=py36_0
- cffi=1.11.5=py36h5e8e0c9_1
- chardet=3.0.4=py36_3
- click=6.7=py_1
- colormath=3.0.0=py_2
- configargparse=0.13.0=py_1
- cryptography=2.3.1=py36hdffb7b8_0
- cryptography-vectors=2.3.1=py36_0
- curl=7.61.0=h93b3f91_1
- cycler=0.10.0=py_1
- dbus=1.13.0=h3a4f0e9_0
- decorator=4.3.0=py_0
- docutils=0.14=py36_0
- dropbox=7.3.1=py36_0
- expat=2.2.5=hfc679d8_1
- fontconfig=2.13.0=h65d0f4c_5
- freetype=2.9.1=h6debe1e_0
- future=0.16.0=py36_2
- gettext=0.19.8.1=0
- glib=2.55.0=h464dc38_2
- google-auth=1.2.1=py_0
- google-auth-httplib2=0.0.2=py36_0
- google-cloud-core=0.24.1=py36_0
- google-cloud-storage=1.1.1=py36_0
- google-resumable-media=0.0.2=py36_0
- googleapis-common-protos=1.5.3=py_1
- gst-plugins-base=1.12.5=hde13a9d_0
- gstreamer=1.12.5=h61a6719_0
- httplib2=0.11.3=py36_0
- icu=58.2=hfc679d8_0
- idna=2.7=py36_2
- idna_ssl=1.0.0=0
- jinja2=2.10=py_1
- jmespath=0.9.3=py_1
- jpeg=9c=h470a237_0
- kiwisolver=1.0.1=py36h2d50403_2
- krb5=1.14.6=0
- libffi=3.2.1=hfc679d8_4
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=7.2.0=hdf63c60_3
- libgfortran=3.0.0=1
- libiconv=1.15=h470a237_2
- libpng=1.6.35=ha92aebf_0
- libprotobuf=3.6.0=hd28b015_0
- libssh2=1.8.0=h5b517e9_2
- libstdcxx-ng=7.2.0=hdf63c60_3
- libuuid=2.32.1=h470a237_0
- libxcb=1.13=h470a237_2
- libxml2=2.9.8=h422b904_3
- lzstring=1.0.3=py36_0
- markdown=2.6.11=py_0
- markupsafe=1.0=py36_0
- matplotlib=2.2.3=py36h8e2386c_0
- multidict=4.3.1=py36h470a237_0
- ncurses=6.1=hfc679d8_1
- networkx=2.0=py36_1
- numpy=1.15.0=py36_blas_openblashd3ea46f_200
- openblas=0.2.20=8
- openjdk=8.0.144=zulu8.23.0.3_2
- openssl=1.0.2o=h470a237_1
- pandas=0.23.4=py36hf8a1672_0
- paramiko=2.1.2=py36_0
- pcre=8.41=h470a237_2
- perl=5.26.2=h470a237_0
- pigz=2.3.4=0
- pip=18.0=py36_1
- prettytable=0.7.2=py_2
- protobuf=3.6.0=py36hfc679d8_0
- psutil=5.4.7=py36_0
- pthread-stubs=0.4=h470a237_1
- pyasn1=0.4.4=py_0
- pycparser=2.18=py_1
- pyparsing=2.2.0=py_1
- pyqt=5.6.0=py36h8210e8a_6
- python=3.6.6=h5001a0f_0
- python-dateutil=2.7.3=py_0
- python-irodsclient=0.7.0=py_0
- pytz=2018.5=py_0
- pyyaml=3.12=py36_1
- qt=5.6.2=hf70d934_9
- ratelimiter=1.2.0=py36_0
- readline=7.0=haf1bffa_1
- requests=2.13.0=py36_0
- s3transfer=0.1.13=py36_0
- setuptools=40.0.0=py36_1
- sip=4.18=py36_1
- six=1.11.0=py36_1
- spectra=0.0.11=py_0
- sqlite=3.24.0=h2f33b56_0
- tk=8.6.8=0
- tornado=5.1=py36h470a237_1
- wheel=0.31.1=py36_1
- wrapt=1.10.11=py36_0
- xmlrunner=1.7.7=py_0
- xorg-libxau=1.0.8=h470a237_6
- xorg-libxdmcp=1.1.2=h470a237_7
- xz=5.2.4=h470a237_1
- yaml=0.1.7=h470a237_1
- yarl=1.2.6=py36h470a237_0
- zlib=1.2.11=h470a237_3
- gzip=1.7=1
prefix: /home/vintache-d/RNAseq_quantif_pipeline/miniconda/envs/rnaSeqQuantif
......@@ -256,7 +256,24 @@
{% endfor %}
<HR align="center" size="6" width="100%">
<!-- Used tools display -->
<header><br/>
<h2 id="toolversions">Tools versions</h2>
</header>
{# Display of the tools used versions #}
<table id="tool-versions" class="display compact" style="width:100%">
<thead>
<tr>
<th>Tool</th>
<th>Version</th>
</tr>
</thead>
</table>
<HR align="center" size="6" width="100%">
<p>This analysis pipeline is provided by <a href="https://pf-bird.univ-nantes.fr/" target="_blank">the BiRD bioinformatics core facility of Nantes</a>.</p>
<p>It is provided "as is" without any warranties of any kind.</p>
<p>The code is hosted on <a href="https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline" target="_blank">the gitlab of the University of Nantes</a>.</p>
</div>
</section>
<!-- End of annexes part -->
......@@ -308,6 +325,16 @@
]
});
}
$(document).ready(function(){
$('#tool-versions').DataTable({
"data":{{toolVersions}},
"columns":[
{"data":"tool"},
{"data":"version"}
]
});
});
</script>
<!-- Barplot HighCharts number of detected genes -->
......
......@@ -138,16 +138,6 @@ dataLabels <- subset(data, label != "")
png(paste(paste(OUTDIR,comp,comp,sep="/"),"Volcano-plot.png",sep="_"),width=10,height=10,units="cm",res=200)
#plot(DE$log2FoldChange,-log10(DE$padj),type="n",ylab="-log10(DEseq padj)",xlab="log2(Fold-Change)",col="black",main=paste0("Volcano plot of comparison ",cond1," (pos FC) VS ",cond2," (neg FC)\nBenjamini & Hochberg method (",nrow(DE.sel$isDE),"/",nrow(DE)," DE genes)"),cex.main=0.5,cex.lab=0.8)
#abline(h=-log10(AdjPValthreshold))
#abline(v = -logFCthreshold)
#abline(v = logFCthreshold)
#mup = do.call(rbind, strsplit(rownames(DE.sel$up), '|',fixed=TRUE))
#mdown = do.call(rbind, strsplit(rownames(DE.sel$down), '|',fixed=TRUE))
#if(nrow(DE.sel$up)>0) text(DE.sel$up$log2FoldChange,-log10(DE.sel$up$padj),labels = mup[,2],cex=.3,col="red")
#if(nrow(DE.sel$down)>0) text(DE.sel$down$log2FoldChange,-log10(DE.sel$down$padj),labels = mdown[,2],cex=.3,col="green")
#points(DE.sel$notDE$log2FoldChange,-log10(DE.sel$notDE$padj),cex=.2,col="black",pch=16)
p <- ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj))) +
geom_point(size = 0.5, color = data$color) +
geom_hline(aes(yintercept=-log10(AdjPValthreshold))) +
......@@ -170,10 +160,6 @@ if (nrow(dataLabels)>0) {
)
}
print(p)
dev.off()
#MA-plot
......
......@@ -26,9 +26,6 @@ config.update(json.load(open(args.samplesFile, "r")))
# Dict() creation for feeding source of the template
templateVars = dict()
# Load configuration file in template
#templateVars["config"] = config
########################
# Project informations #
########################
......@@ -122,6 +119,23 @@ for c in conditionVS:
# Insert counts of DEG in a variable in order to print ma-plot, volcano-plot and deseq table in report if necessary
templateVars["deseqres"][c["condition1"]+"__vs__"+c["condition2"]]["counts"] = count
#################
# Tools listing #
#################
# Recovery of versions.sh results
pack = os.popen("bash "+os.path.join(sys.path[0],"versions.sh"),'r')
packages = pack.read()
pack.close()
templateVars["toolVersions"] = list()
for pack in packages.split("\n"):
if(not pack): continue
toolver = dict()
tool,version = pack.split(":")
toolver["tool"] = tool
toolver["version"] = version
templateVars["toolVersions"].append(toolver)
############
# TEMPLATE #
############
......
#$ -s /bin/bash
#$ -cwd
#$ -V
......
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