src/.conda_envs/splicing_lore_env

-/Xnfs/lbmcdb/common/conda/envs/splicing_lore_env
\ No newline at end of file

src/.conda_envs/sra-tools_2.8.2

-/Xnfs/lbmcdb/common/conda/envs/sra-tools_2.8.2
\ No newline at end of file

src/.conda_envs/star_2.5.3a

-/Xnfs/lbmcdb/common/conda/envs/star_2.5.3a
\ No newline at end of file

src/.conda_envs/star_2.7.0e

-/Xnfs/lbmcdb/common/conda/envs/star_2.7.0e
\ No newline at end of file

src/.conda_envs/star_2.7.3a

-/Xnfs/lbmcdb/common/conda/envs/star_2.7.3a
\ No newline at end of file

src/.conda_envs/subread_1.6.4

-/Xnfs/lbmcdb/common/conda/envs/subread_1.6.4
\ No newline at end of file

src/.conda_envs/tophat_2.1.1

-/Xnfs/lbmcdb/common/conda/envs/tophat_2.1.1
\ No newline at end of file

src/.conda_envs/trimmomatic_0.36

-/Xnfs/lbmcdb/common/conda/envs/trimmomatic_0.36
\ No newline at end of file

src/.conda_envs/trimmomatic_0.39

-/Xnfs/lbmcdb/common/conda/envs/trimmomatic_0.39
\ No newline at end of file

src/.conda_envs/ucsc_375

-/Xnfs/lbmcdb/common/conda/envs/ucsc_375
\ No newline at end of file

src/.conda_envs/umitools_0.3.4

-/Xnfs/lbmcdb/common/conda/envs/umitools_0.3.4
\ No newline at end of file

src/.conda_envs/urqt_d62c1f8

-/Xnfs/lbmcdb/common/conda/envs/urqt_d62c1f8
\ No newline at end of file

src/.conda_packages.sh

-source src/.conda_psmn.sh
-CONDA_ENVS=src/.conda_envs/
-if [ ! -d ${CONDA_ENVS}pigz_2.3.4 ]; then
-  conda create --yes --name pigz_2.3.4 pigz=2.3.4
-fi
-if [ ! -d ${CONDA_ENVS}tophat_2.1.1 ]; then
-  conda create --yes --name tophat_2.1.1 tophat=2.1.1
-fi
-if [ ! -d ${CONDA_ENVS}hisat2_2.0.0 ]; then
-  conda create --yes --name hisat2_2.0.0 hisat2=2.0.0 samtools=1.7
-fi
-if [ ! -d ${CONDA_ENVS}hisat2_2.1.0 ]; then
-  conda create --yes --name hisat2_2.1.0 hisat2=2.1.0 samtools=1.7
-fi
-if [ ! -d ${CONDA_ENVS}rsem_1.3.1 ]; then
-  conda create --yes --name rsem_1.3.1 rsem=1.3.1 samtools=1.3
-fi
-if [ ! -d ${CONDA_ENVS}rsem_1.3.0 ]; then
-  conda create --yes --name rsem_1.3.0 rsem=1.3.0 samtools=1.3
-fi
-if [ ! -d ${CONDA_ENVS}samblaster_0.1.24 ]; then
-  conda create --yes --name samblaster_0.1.24 samblaster=0.1.24
-fi
-if [ ! -d ${CONDA_ENVS}nextflow_0.25.1 ]; then
-  conda create --yes --name nextflow_0.25.1 nextflow=0.25.1
-fi
-if [ ! -d ${CONDA_ENVS}nextflow_19.01.0 ]; then
-  conda create --yes --name nextflow_19.01.0 nextflow=19.01.0
-fi
-if [ ! -d ${CONDA_ENVS}nextflow_0.32.0 ]; then
-  conda create --yes --name nextflow_0.32.0 nextflow=0.32.0
-fi
-if [ ! -d ${CONDA_ENVS}nextflow_0.28.2 ]; then
-  conda create --yes --name nextflow_0.28.2 nextflow=0.28.2
-fi
-if [ ! -d ${CONDA_ENVS}samtools_1.7 ]; then
-  conda create --yes --name samtools_1.7 samtools=1.7
-fi
-if [ ! -d ${CONDA_ENVS}samtools_1.5 ]; then
-  conda create --yes --name samtools_1.5 samtools=1.5
-fi
-if [ ! -d ${CONDA_ENVS}bowtie2_2.3.2 ]; then
-  conda create --yes --name bowtie2_2.3.2 bowtie2=2.3.2 samtools=1.7
-fi
-if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
-  conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
-fi
-if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
-  conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
-fi
-if [ ! -d ${CONDA_ENVS}trimmomatic_0.36 ]; then
-  conda create --yes --name trimmomatic_0.36 trimmomatic=0.36
-fi
-if [ ! -d ${CONDA_ENVS}trimmomatic_0.39 ]; then
-  conda create --yes --name trimmomatic_0.39 trimmomatic=0.39
-fi
-if [ ! -d ${CONDA_ENVS}Python_3.6.1 ]; then
-  conda create --yes --name Python_3.6.1 Python=3.6.1
-fi
-if [ ! -d ${CONDA_ENVS}Python_2.7.13 ]; then
-  conda create --yes --name Python_2.7.13 Python=2.7.13
-fi
-if [ ! -d ${CONDA_ENVS}kallisto_0.44.0 ]; then
-  conda create --yes --name kallisto_0.44.0 kallisto=0.44.0
-fi
-if [ ! -d ${CONDA_ENVS}kallisto_0.43.1 ]; then
-  conda create --yes --name kallisto_0.43.1 kallisto=0.43.1
-fi
-if [ ! -d ${CONDA_ENVS}music_1.0.0 ]; then
-  conda create --yes --name music_1.0.0 music=1.0.0
-fi
-if [ ! -d ${CONDA_ENVS}umitools_0.3.4 ]; then
-  conda create --yes --name umitools_0.3.4 umitools=0.3.4
-fi
-if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
-  conda create --yes --name fastp_0.19.7 fastp=0.19.7
-fi
-if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
-  conda create --yes --name gatk_3.8 gatk=3.8
-fi
-if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
-  conda create --yes --name cutadapt_1.14 cutadapt=1.14
-fi
-if [ ! -d ${CONDA_ENVS}bioawk_1.0 ]; then
-  conda create --yes --name bioawk_1.0 bioawk=1.0
-fi
-if [ ! -d ${CONDA_ENVS}canu_1.7 ]; then
-  conda create --yes --name canu_1.7 canu=1.7
-fi
-if [ ! -d ${CONDA_ENVS}fastqc_0.11.5 ]; then
-  conda create --yes --name fastqc_0.11.5 fastqc=0.11.5
-fi
-if [ ! -d ${CONDA_ENVS}bedtools_2.25.0 ]; then
-  conda create --yes --name bedtools_2.25.0 bedtools=2.25.0
-fi
-if [ ! -d ${CONDA_ENVS}macs2_2.1.2 ]; then
-  conda create --yes --name macs2_2.1.2 macs2=2.1.2
-fi
-if [ ! -d ${CONDA_ENVS}bcftools_1.7 ]; then
-  conda create --yes --name bcftools_1.7 bcftools=1.7
-fi
-if [ ! -d ${CONDA_ENVS}salmon_0.8.2 ]; then
-  conda create --yes --name salmon_0.8.2 salmon=0.8.2
-fi
-if [ ! -d ${CONDA_ENVS}urqt_d62c1f8 ]; then
-  conda create --yes --name urqt_d62c1f8 urqt=d62c1f8
-fi
-if [ ! -d ${CONDA_ENVS}multiqc_0.9 ]; then
-  conda create --yes --name multiqc_0.9 multiqc=0.9
-fi
-if [ ! -d ${CONDA_ENVS}multiqc_1.7 ]; then
-  conda create --yes --name multiqc_1.7 multiqc=1.7
-fi
-if [ ! -d ${CONDA_ENVS}multiqc_1.0 ]; then
-  conda create --yes --name multiqc_1.0 multiqc=1.0
-fi
-if [ ! -d ${CONDA_ENVS}cdhit_4.6.8 ]; then
-  conda create --yes --name cdhit_4.6.8 cdhit=4.6.8
-fi
-if [ ! -d ${CONDA_ENVS}deeptools_3.0.2 ]; then
-  conda create --yes --name deeptools_3.0.2 deeptools=3.0.2
-fi
-if [ ! -d ${CONDA_ENVS}htseq_0.9.1 ]; then
-  conda create --yes --name htseq_0.9.1 htseq=0.9.1
-fi
-if [ ! -d ${CONDA_ENVS}htseq_0.11.2 ]; then
-  conda create --yes --name htseq_0.11.2 htseq=0.11.2
-fi
-if [ ! -d ${CONDA_ENVS}R_3.4.3 ]; then
-  conda create --yes --name R_3.4.3 R=3.4.3
-fi
-if [ ! -d ${CONDA_ENVS}R_3.3.1 ]; then
-  conda create --yes --name R_3.3.1 R=3.3.1
-fi
-if [ ! -d ${CONDA_ENVS}file_handle_0.1.1 ]; then
-  conda create --yes --name file_handle_0.1.1 file_handle=0.1.1
-fi
-if [ ! -d ${CONDA_ENVS}ncdu_1.13 ]; then
-  conda create --yes --name ncdu_1.13 ncdu=1.13
-fi
-if [ ! -d ${CONDA_ENVS}picard_2.18.11 ]; then
-  conda create --yes --name picard_2.18.11 picard=2.18.11
-fi
-if [ ! -d ${CONDA_ENVS}sambamba_0.6.7 ]; then
-  conda create --yes --name sambamba_0.6.7 sambamba=0.6.7
-fi
-if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
-  conda create --yes --name star_2.7.3a star=2.7.3a
-fi

src/.conda_psmn.sh

-/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file

src/.docker_modules/CITE-seq-Count/1.4.5/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:22.04
+
+ENV CITESEQ_VERSION=1.4.5
+ENV PACKAGES procps locales gcc libstdc++-10-dev libcurl4 libc6 python3 python3-pip python3-dev
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install CITE-seq-Count==${CITESEQ_VERSION}
+

src/.docker_modules/CITE-seq-Count/1.4.5/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/cite_seq_count:1.4.5
+docker build src/.docker_modules/CITE-seq-Count/1.4.5 -t 'lbmc/cite_seq_count:1.4.5'
+docker push lbmc/cite_seq_count:1.4.5
+# docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cite_seq_count:1.4.5" --push src/.docker_modules/CITE-seq-Count/1.4.5

src/.docker_modules/CITE-seq-Count/1.5.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:22.04
+
+ENV PACKAGES procps locales gcc libstdc++-10-dev libcurl4 libc6 python3 python3-pip python3-dev git
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+RUN git clone https://github.com/Hoohm/CITE-seq-Count.git \
+    && cd CITE-seq-Count \
+    && git checkout 1.5.0-alpha \
+    && pip3 install requests pooch \
+    && pip3 install ./
+

src/.docker_modules/CITE-seq-Count/1.5.0/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/cite_seq_count:1.5.0
+docker build src/.docker_modules/CITE-seq-Count/1.5.0 -t 'lbmc/cite_seq_count:1.5.0'
+docker push lbmc/cite_seq_count:1.5.0
+# docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cite_seq_count:1.5.0" --push src/.docker_modules/CITE-seq-Count/1.5.0

src/.docker_modules/agat/0.8.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0 
\ No newline at end of file

src/.docker_modules/agat/0.8.0/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/agat:0.8.0
+# docker build src/.docker_modules/agat/0.8.0 -t 'lbmc/agat:0.8.0'
+# docker push lbmc/agat:0.8.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/agat:0.8.0" --push src/.docker_modules/agat/0.8.0