src/docker_modules/Kallisto/0.44.0/Dockerfile → src/.docker_modules/kallisto/0.44.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 

src/.docker_modules/kallisto/0.44.0/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/kallisto:0.44.0
+# docker build src/.docker_modules/kallisto/0.44.0 -t 'lbmc/kallisto:0.44.0'
+# docker push lbmc/kallisto:0.44.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/kallisto:0.44.0" --push src/.docker_modules/kallisto/0.44.0

src/.docker_modules/kallistobustools/0.24.4/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.7
+MAINTAINER Laurent Modolo
+
+ENV KB_VERSION=0.24.4
+
+RUN pip3 install kb_python==${KB_VERSION}
+ENTRYPOINT ["/bin/sh"]
+RUN ln -s /usr/local/lib/python3.7/site-packages/kb_python/bins/linux/bustools/bustools /usr/local/bin/
+RUN ln -s /usr/local/lib/python3.7/site-packages/kb_python/bins/linux/kallisto/kallisto /usr/local/bin/

src/.docker_modules/kallistobustools/0.24.4/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/kallistobustools:0.24.4
+# docker build src/.docker_modules/kallistobustools/0.24.4 -t 'lbmc/kallistobustools:0.24.4'
+# docker push lbmc/kallistobustools:0.24.4
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/kallistobustools:0.24.4" --push src/.docker_modules/kallistobustools/0.24.4

src/.docker_modules/kallistobustools/0.39.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.8-alpine
+MAINTAINER Laurent Modolo
+
+ENV B_VERSION=0.39.3
+ENV K_VERSION=0.46.1
+
+RUN apk add  --update --no-cache bash musl-dev linux-headers g++ cmake make build-base hdf5 hdf5-dev zlib-dev autoconf bash && \
+wget https://github.com/BUStools/bustools/archive/v${B_VERSION}.tar.gz && \
+tar xvf v${B_VERSION}.tar.gz && \
+cd bustools-${B_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+sed -i -e 's/"Common\.hpp"/"Common\.hpp"\n#include <cmath>/g' ../src/bustools_whitelist.h && \
+sed -i 's/pow/std::pow/g' ../src/bustools_whitelist.cpp && \
+make && \
+make install && \
+wget https://github.com/pachterlab/kallisto/archive/v${K_VERSION}.tar.gz && \
+tar xvf v${K_VERSION}.tar.gz && \
+cd kallisto-${K_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+make && \
+make install && \
+wget https://github.com/BUStools/getting_started/releases/download/getting_started/t2g.py && \
+chmod +x t2g.py && \
+mv t2g.py /usr/local/bin/ && \
+rm -R kallisto* bustools* v${K_VERSION}.tar.gz v${B_VERSION}.tar.gz
+
+CMD ["sh"]

src/.docker_modules/kallistobustools/0.39.3/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/kallistobustools:0.39.3
+# docker build src/.docker_modules/kallistobustools/0.39.3 -t 'lbmc/kallistobustools:0.39.3'
+# docker push lbmc/kallistobustools:0.39.3
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/kallistobustools:0.39.3" --push src/.docker_modules/kallistobustools/0.39.3

src/.docker_modules/kb/0.26.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.9-slim 
+
+ENV KB_VERSION="0.26.0"
+
+RUN apt update && apt install -y procps && pip3 install kb-python==${KB_VERSION}
+
+COPY t2g.py /usr/bin/
+COPY fix_t2g.py /usr/bin/
+
+RUN chmod +x /usr/bin/t2g.py
+RUN chmod +x /usr/bin/fix_t2g.py
+
+CMD [ "bash" ]

src/.docker_modules/kb/0.26.0/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/kb:0.26.0
+# docker build src/.docker_modules/kb/0.26.0 -t 'lbmc/kb:0.26.0'
+# docker push lbmc/kb:0.26.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/kb:0.26.0" --push src/.docker_modules/kb/0.26.0

src/.docker_modules/kb/0.26.0/fix_t2g.py

+#!/usr/local/bin/python
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+import os
+import re
+import gzip
+import argparse
+
+
+def validate_file(f):
+    if not os.path.exists(f):
+        # Argparse uses the ArgumentTypeError to give a rejection message like:
+        # error: argument input: x does not exist
+        raise argparse.ArgumentTypeError("{0} does not exist".format(f))
+    return f
+
+
+def t2g_line(transcript, gene):
+    return str(transcript) + "\t" + str(gene) + "\n"
+
+
+def build_t2g_re():
+    return re.compile("([A-Z]+[0-9]+)\.\S+\s([A-Z]+[0-9]+)\.\S+")
+
+
+def get_t2g(line, t2g_re):
+    return t2g_re.match(line)
+
+
+def get_t2g_line(line, t2g_re):
+    t2g_id = get_t2g(line, t2g_re)
+    return {'transcript_id': t2g_id, 'gene_id': t2g_id}
+
+
+def write_t2g_line(t2g, line, t2g_re):
+    results = get_t2g_line(line, t2g_re)
+    if results['transcript_id']:
+        t2g.write(
+            t2g_line(
+                results['transcript_id'].group(1),
+                results['gene_id'].group(2)
+            )
+        )
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="create transcript to genes file from a gtf file."
+    )
+    parser.add_argument(
+        "-f", "--t2g", dest="t2g", required=True, type=validate_file,
+        help="t2g file", metavar="FILE"
+    )
+    args = parser.parse_args()
+    t2g_re = build_t2g_re()
+
+    try:
+        with gzip.open(args.t2g, "rb") as gtf:
+            with open("fix_t2g.txt", "w") as t2g:
+                for line in gtf:
+                    write_t2g_line(t2g, str(line), t2g_re)
+    except gzip.BadGzipFile:
+        with open(args.t2g, "r") as gtf:
+            with open("fix_t2g.txt", "w") as t2g:
+                for line in gtf:
+                    write_t2g_line(t2g, str(line), t2g_re)

src/.docker_modules/kb/0.26.0/t2g.py

+#!/usr/local/bin/python
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+import os
+import re
+import gzip
+import argparse
+
+
+def validate_file(f):
+    if not os.path.exists(f):
+        # Argparse uses the ArgumentTypeError to give a rejection message like:
+        # error: argument input: x does not exist
+        raise argparse.ArgumentTypeError("{0} does not exist".format(f))
+    return f
+
+
+def t2g_line(transcript, gene):
+    return str(transcript) + "\t" + str(gene) + "\n"
+
+
+def build_gene_re():
+    return re.compile(".*gene_id\s+\"(\S+)\";.*")
+
+
+def build_transcript_re():
+    return re.compile(".*transcript_id\s+\"(\S+)\";.*")
+
+
+def get_gene(line, gene_re):
+    return gene_re.match(line)
+
+
+def get_transcript(line, transcript_re):
+    return transcript_re.match(line)
+
+
+def gtf_line(line, transcript_re, gene_re):
+    transcript_id = get_transcript(line, transcript_re)
+    gene_id = get_gene(line, gene_re)
+    return {'transcript_id': transcript_id, 'gene_id': gene_id}
+
+
+def write_t2g_line(t2g, line, transcript_re, gene_re):
+    results = gtf_line(line, transcript_re, gene_re)
+    if results['transcript_id']:
+        t2g.write(
+            t2g_line(
+                results['transcript_id'].group(1),
+                results['gene_id'].group(1)
+            )
+        )
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="create transcript to genes file from a gtf file."
+    )
+    parser.add_argument(
+        "-g", "--gtf", dest="gtf", required=True, type=validate_file,
+        help="gtf file", metavar="FILE"
+    )
+    args = parser.parse_args()
+    gene_re = build_gene_re()
+    transcript_re = build_transcript_re()
+
+    try:
+        with gzip.open(args.gtf, "rb") as gtf:
+            with open("t2g_dup.txt", "w") as t2g:
+                for line in gtf:
+                    write_t2g_line(t2g, str(line), transcript_re, gene_re)
+    except gzip.BadGzipFile:
+        with open(args.gtf, "r") as gtf:
+            with open("t2g_dup.txt", "w") as t2g:
+                for line in gtf:
+                    write_t2g_line(t2g, str(line), transcript_re, gene_re)
+

src/.docker_modules/kb/0.26.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.9-slim 
+
+ENV KB_VERSION="0.26.3"
+
+RUN apt update && apt install -y procps make gcc zlib1g-dev libbz2-dev  	libcurl4 liblzma-dev \
+        && pip3 install pysam anndata h5py Jinja2 loompy nbconvert nbformat ngs-tools numpy pandas plotly scanpy scikit-learn tqdm \
+        && pip3 install kb-python==${KB_VERSION} gffutils
+
+COPY t2g.py /usr/bin/
+
+RUN chmod +x /usr/bin/t2g.py
+
+CMD [ "bash" ]

src/.docker_modules/kb/0.26.3/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/kb:0.26.3
+docker build src/.docker_modules/kb/0.26.3 -t 'lbmc/kb:0.26.3'
+docker push lbmc/kb:0.26.3

src/.docker_modules/kb/0.26.3/t2g.py

+#!/usr/local/bin/python
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+import os
+import gffutils
+import argparse
+
+
+def validate_file(f):
+    if not os.path.exists(f):
+        # Argparse uses the ArgumentTypeError to give a rejection message like:
+        # error: argument input: x does not exist
+        raise argparse.ArgumentTypeError("{0} does not exist".format(f))
+    return f
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="create transcript to genes file from a gtf file."
+    )
+    parser.add_argument(
+        "-g", "--gtf", dest="gtf", required=True, type=validate_file,
+        help="gtf file", metavar="FILE"
+    )
+    args = parser.parse_args()
+
+    db = gffutils.create_db(
+        args.gtf,
+        dbfn=":memory:",
+        force=True,
+        merge_strategy="merge",
+        disable_infer_transcripts=False,
+        disable_infer_genes=False
+    )
+    with open("t2g.txt", "w") as t2g:
+        for gene in db.all_features():
+            for transcript in db.children(
+              gene, featuretype='transcript', order_by='start'
+            ):
+                t2g_line = str(transcript["transcript_id"][0]) + \
+                    "\t" + \
+                    str(gene["gene_id"][0])
+                t2g_line = t2g_line.split("\t")
+                t2g.write(
+                    str(t2g_line[0].split(".")[0]) +
+                    "\t" +
+                    str(t2g_line[1].split(".")[0]) +
+                    "\n"
+                )

src/.docker_modules/last/1060/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV LAST_VERSION=1060
+ENV PACKAGES curl=7.58.0* \
+    unzip \
+    make=4.1* \
+    g++ \
+    zlib1g-dev=1:1.2.11* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    python
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L http://last.cbrc.jp/last-${LAST_VERSION}.zip -o last-${LAST_VERSION}.zip && \
+unzip last-${LAST_VERSION}.zip && \
+cd last-${LAST_VERSION} && \
+make && \
+cp src/last* /usr/bin/ && \
+cp scripts/* /usr/bin/ && \
+cd .. && \
+rm -Rf last-${LAST_VERSION}

src/.docker_modules/last/1060/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/last:1060
+# docker build src/.docker_modules/last/1060/ -t 'lbmc/last:1060'
+# docker push lbmc/last:1060
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/last:1060" --push src/.docker_modules/last/1060

src/.docker_modules/liftover/357/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/ucsc-liftover:357--1
+MAINTAINER Laurent Modolo

src/.docker_modules/liftover/357/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/liftover:357
+# docker build src/.docker_modules/liftover/357/ -t 'lbmc/liftover:357'
+# docker push lbmc/liftover:357
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/liftover:357" --push src/.docker_modules/liftover/357

src/.docker_modules/macs2/2.1.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1
+MAINTAINER Laurent Modolo

src/.docker_modules/macs2/2.1.2/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/macs2:2.1.2
+# docker build src/.docker_modules/macs2/2.1.2 -t 'lbmc/macs2:2.1.2'
+# docker push lbmc/macs2:2.1.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/macs2:2.1.2" --push src/.docker_modules/macs2/2.1.2

src/.docker_modules/macs3/3.0.0a6/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.9-slim
+MAINTAINER Laurent Modolo
+
+ENV MACS3_VERSION=3.0.0a6
+RUN apt-get update -qq \
+    && apt-get install --no-install-recommends --yes \
+        build-essential \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libcurl4-gnutls-dev \
+        libssl-dev \
+        libncurses5-dev \
+        procps
+RUN pip install macs3==${MACS3_VERSION}