Dockerfiles

This repository contains Dockerfile used to make Docker images used at Genomic Paris Centre.

Name	Name	Last commit message	Last commit date
Latest commit jourdren ADD Dockerfile for Guppy 6.0.1 Feb 22, 2022 3bb664c · Feb 22, 2022 History 398 Commits
Lineage/lineage-monocle	Lineage/lineage-monocle	SCE update	Jul 30, 2018
MAST/1.0.5	MAST/1.0.5	update dockerfile	May 3, 2018
Monocle	Monocle	SCE update	Jul 12, 2018
Rsubread/1.18.0	Rsubread/1.18.0	Dockerfile to create a container image for Rsubread	May 29, 2015
SARTools	SARTools	Dockerfile to build SARTools 1.3.2 images	Aug 2, 2016
SCPattern/0.0.4	SCPattern/0.0.4	Create Dockerfile for SCPattern 0.0.4 images	Aug 18, 2016
Seurat	Seurat	Update R dependancies	Jul 31, 2018
Sincell/1.6.0	Sincell/1.6.0	Update dockerfile	May 10, 2018
UMI-tools	UMI-tools	ADD: Add Dockerfile for UMI-tools 0.5.3.	Mar 26, 2018
albacore	albacore	ADD: Add Dockerfile for albacore-2.3.4.	Dec 14, 2018
alignqc	alignqc	alignqc v2.0.4	Oct 26, 2017
babel	babel	Dockerfile for Babel 0.3-0 image	Aug 1, 2016
bamqc/20160127	bamqc/20160127	Add alignqc and bamqc dockerfile	Mar 20, 2017
bcbb-gff/0.6.2	bcbb-gff/0.6.2	dockerfile fo gff parser python library by Chapman	Oct 5, 2015
bcbio-nextgen/1.0.0a0	bcbio-nextgen/1.0.0a0	Dockerfile bcbio-nextgen 1.0.0a0	Jul 27, 2016
bcl2fastq/bcl2fastq-1.8.4	bcl2fastq/bcl2fastq-1.8.4	ADD new version of bcl2fastq software, versio 1.8.4.	Mar 27, 2015
bcl2fastq2	bcl2fastq2	Add Dockerfile for bcl2fastq 2.20.0.422.	Sep 6, 2017
bed2bigbed	bed2bigbed	add hg38 chrom sizes.	Jul 4, 2016
bedops/2.4.14	bedops/2.4.14	correction for path	Jul 17, 2015
bedtools	bedtools	ADD: Add Dockerfile for Bedtools 2.27.1.	Mar 26, 2018
biomart/2.26.1	biomart/2.26.1	Dockerfile to build biomaRt container	Mar 3, 2016
bioperl/bioperl-1.6.924	bioperl/bioperl-1.6.924	FIX : Reorganised in version subdirectory	Mar 3, 2015
biopython/1.63-1	biopython/1.63-1	add gff parsing lib and pyfasta to the container	Oct 6, 2015
bioservices	bioservices	bioservices 1.4.15	Jan 27, 2017
biotoolbox	biotoolbox	Dockerfile to build a biotoolbox 1.35 container with Ensembl 83 api	Mar 3, 2016
blacklistremove	blacklistremove	Add blacklistremove 1.1 and restore 1.0 version.	Jun 27, 2018
blast+/2.2.28	blast+/2.2.28	ADD: Add blast 2.2.26 and blast+ 2.2.28 Dockerfiles.	Aug 22, 2016
blast2/2.2.26	blast2/2.2.26	ADD: Add blast 2.2.26 and blast+ 2.2.28 Dockerfiles.	Aug 22, 2016
bowtie	bowtie	Add Dockerfiles for Bowtie1 Bowtie2 and Cutadapt	Mar 24, 2015
bwa	bwa	bug correction	Oct 21, 2016
casava/casava-1.8.2	casava/casava-1.8.2	first commit	Jun 24, 2014
cite-seq-count/v1.4.1	cite-seq-count/v1.4.1	Add CITE-seq-Count Dockerfile	Jan 29, 2019
cutadapt	cutadapt	ADD Dockerfile for Cutadapt 2.10	Oct 2, 2020
deepbinner/0.2.0	deepbinner/0.2.0	ADD Dockerfile for deepbinner 0.2.0	Jan 29, 2019
deeptools	deeptools	ADD: Add Dockerfile for DeepTools 2.5.7.	Mar 26, 2018
deseq	deseq	ADD Dockerfile for DESeq2 1.30.0	Nov 5, 2020
dwgsim/dwgsim-0.1.11	dwgsim/dwgsim-0.1.11	FIX : $PATH problems	Mar 5, 2015
eoulsan/eoulsan-1.2.2	eoulsan/eoulsan-1.2.2	first commit	Jun 24, 2014
express/express-1.5.1	express/express-1.5.1	FIX : Reorganised in version subdirectory	Mar 3, 2015
fastqc	fastqc	ADD: FastQC 0.11.5 Dockerfile.	Aug 1, 2016
genometools	genometools	dockerfile to make genometools-1.5.9 image	Jul 19, 2018
gff3-ptools/gff3-ptools-0.4.0	gff3-ptools/gff3-ptools-0.4.0	FIX : wget was missing	Mar 3, 2015
ggplot2	ggplot2	SCE update	Jul 27, 2018
gmap/2017-02-15	gmap/2017-02-15	ADD: Add Dockerfile for gmap/gsnap 2017-02-15.	Mar 26, 2017
guppy-gpu	guppy-gpu	ADD Dockerfile for Guppy 6.0.1	Feb 22, 2022
guppy	guppy	ADD Dockerfile for Guppy 6.0.1	Feb 22, 2022
hgcolor	hgcolor	Dockerfile for HG-ColoR	Jul 11, 2017
hisat/0.1.5-beta	hisat/0.1.5-beta	ADD: Add HISAT 0.1.5-beta	Apr 1, 2015
htseq	htseq	ADD: Add Dockerfiles for HTSeq 0.10.0 and 0.11.0.	Oct 3, 2018
k8/0.2.4	k8/0.2.4	ADD: Add Dockerfile for k8 0.2.4.	Sep 3, 2018
kentutils/302.1.0	kentutils/302.1.0	ADD: Dockerfile for kentutils.	Dec 7, 2015
macs	macs	ADD: Add MACS2 2.1.0.20140616.	Feb 25, 2015
marginAlign/0.1	marginAlign/0.1	docker image for marginAlign 20181029	Dec 11, 2018
matplotlib/1.4.3	matplotlib/1.4.3	Dockerfile for matplotlib building containers	Aug 6, 2015
minimap2/v2.3	minimap2/v2.3	minimap v2.3	Oct 26, 2017
miso/miso-0.5.3	miso/miso-0.5.3	Delete miso/0.5.3 directory	Apr 10, 2015
nanook/0.79	nanook/0.79	Add the possibility to configure JAVA_ARGS	Oct 24, 2016
nanopack	nanopack	Upgrade of all modules	Jan 14, 2019
olb/olb-1.9.4	olb/olb-1.9.4	first commit	Jun 24, 2014
ont-fast5-api	ont-fast5-api	ADD Dockerfile for ont-fast5-api 1.3.0	Apr 2, 2019
paftools/2.9	paftools/2.9	ADD: Add Dockerfile for paftools 2.9.	Mar 16, 2018
picard/1.134	picard/1.134	ADD: Add picard 1.134.	Jun 30, 2015
pinfish/master	pinfish/master	Update Dockerfile	Jan 4, 2019
porechop	porechop	ADD Dockerfile for porechop 0.2.4	Jan 30, 2019
poretools/0.6.0	poretools/0.6.0	Try to make it work...	Nov 10, 2016
proovread/2.14.0	proovread/2.14.0	Dockerfile for proovread 2.14.0	May 30, 2017
ribomap/1.2	ribomap/1.2	Dockerfile and bash script to build Ribomap 1.2 images & run it with …	Aug 2, 2016
ribopicker/0.4.3	ribopicker/0.4.3	Dockerfile to build ribopicker 0.4.3 container	Mar 3, 2016
riboproanalysis/1.0.0	riboproanalysis/1.0.0	FIX: download bcl2fastq rpm file, now source is the Illumina web site.	Aug 31, 2015
rsem	rsem	Fix the previous Dockerfile	Mar 4, 2016
samtools	samtools	UPDATE: Update Dockerfile for samtools 1.4.1 to use universe Ubuntu d…	Nov 9, 2017
scClustering/seurat-clustering	scClustering/seurat-clustering	SCE Update	Jul 31, 2018
scDGE/dge-scde	scDGE/dge-scde	SCE update	Jul 30, 2018
scdd	scdd	SCE update	Jul 11, 2018
scde	scde	SCE update	Jul 11, 2018
scpoolednormalization	scpoolednormalization	SCE update	Jul 30, 2018
scqualitychecking	scqualitychecking	Treat cleanup error	Jul 30, 2018
scran	scran	Change base image	Jul 30, 2018
singlecellexperiment/3.7	singlecellexperiment/3.7	ADD: Add Docker file for singlecellexperiment 3.7.	Jun 14, 2018
star	star	STAR 2.5.2b	Feb 7, 2017
subread	subread	dockerfile for subread 1.6.2	Sep 20, 2018
sumNormalization	sumNormalization	SCE update	Jul 30, 2018
tophat2/2.0.14	tophat2/2.0.14	Soumission de TopHat2 avec Bowtie 2.2.3	Apr 24, 2015
trimgalore/0.4.1	trimgalore/0.4.1	FIX: For trimgalore 0.4.1, update to rename output files for handling…	Nov 28, 2019
velocyto	velocyto	change tag	Dec 18, 2018
README.md	README.md	first commit	Jun 24, 2014

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