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#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/umi_tools:1.0.0
# docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
# docker push lbmc/umi_tools:1.0.0
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/umi_tools:1.0.0" --push src/.docker_modules/umi_tools/1.0.0
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM ubuntu:18.04 FROM ubuntu:18.04
MAINTAINER Laurent Modolo MAINTAINER Laurent Modolo
ENV PACKAGES git=1:2.17.0* \ ENV URQT_VERSION=d62c1f8
ENV PACKAGES git=1:2.17* \
build-essential=12.4* \ build-essential=12.4* \
ca-certificates=20180409 \ ca-certificates=20180409 \
procps \
zlib1g-dev=1:1.2.11* zlib1g-dev=1:1.2.11*
RUN apt-get update && \ RUN apt-get update && \
......
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/urqt:d62c1f8
# docker build src/.docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
# docker push lbmc/urqt:d62c1f8
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/urqt:d62c1f8" --push src/.docker_modules/urqt/d62c1f8
/sps/lbmc/common/singularity/
\ No newline at end of file
/Xnfs/abc/singularity/
\ No newline at end of file
#!/bin/sh
docker build src/nf_modules/BEDtools/2.25.0 -t 'bedtools:2.25.0'
#!/bin/sh
docker build src/nf_modules/Bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
nextflow src/nf_modules/Bowtie2/tests/index.nf \
-c src/nf_modules/Bowtie2/bowtie2.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
nextflow src/nf_modules/Bowtie2/tests/mapping_single.nf \
-c src/nf_modules/Bowtie2/bowtie2.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
nextflow src/nf_modules/Bowtie2/tests/mapping_paired.nf \
-c src/nf_modules/Bowtie2/bowtie2.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
#!/bin/sh
docker build src/nf_modules/FastQC/0.11.5 -t 'fastqc:0.11.5'
#!/bin/sh
docker build src/nf_modules/HTSeq/0.8.0 -t 'htseq:0.8.0'
nextflow src/nf_modules/HTSeq/tests/counting.nf \
-c src/nf_modules/HTSeq/htseq.config \
-profile docker \
--gtf "data/tiny_dataset/annot/tiny.gff" \
--bam "data/tiny_dataset/map/tiny_v2.bam"
#!/bin/sh
docker build src/nf_modules/Kallisto/0.43.1 -t 'kallisto:0.43.1'
nextflow src/nf_modules/Kallisto/tests/index.nf \
-c src/nf_modules/Kallisto/kallisto.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
nextflow src/nf_modules/Kallisto/tests/mapping_single.nf \
-c src/nf_modules/Kallisto/kallisto.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
nextflow src/nf_modules/Kallisto/tests/mapping_paired.nf \
-c src/nf_modules/Kallisto/kallisto.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
#!/bin/sh
docker build src/nf_modules/MultiQC/1.0 -t 'multiqc:1.0'
#!/bin/sh
docker build src/nf_modules/RSEM/1.3.0 -t 'rsem:1.3.0'
nextflow src/nf_modules/RSEM/tests/index.nf \
-c src/nf_modules/RSEM/rsem.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--annotation "data/tiny_dataset/annot/tiny.gff"
nextflow src/nf_modules/RSEM/tests/quantification_single.nf \
-c src/nf_modules/RSEM/rsem.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
nextflow src/nf_modules/RSEM/tests/quantification_paired.nf \
-c src/nf_modules/RSEM/rsem.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
#!/bin/sh
docker build src/nf_modules/SAMtools/1.7 -t 'samtools:1.7'
nextflow src/nf_modules/SAMtools/tests/sort_bams.nf \
-c src/nf_modules/SAMtools/samtools.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam"
nextflow src/nf_modules/SAMtools/tests/index_bams.nf \
-c src/nf_modules/SAMtools/samtools.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.sort.bam"
nextflow src/nf_modules/SAMtools/tests/split_bams.nf \
-c src/nf_modules/SAMtools/samtools.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam"
nextflow src/nf_modules/SAMtools/tests/filter_bams.nf \
-c src/nf_modules/SAMtools/samtools.config \
-profile docker \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
--bed "data/tiny_dataset/OLD/2genes.bed"
#!/bin/sh
docker build src/nf_modules/SRAtoolkit/2.8.2 -t 'sratoolkit:2.8.2'
#!/bin/sh
docker build src/nf_modules/Salmon/0.8.2 -t 'salmon:0.8.2'