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
 

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 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
 

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 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==${KB_VERSION} gffutils==0.10.1
+RUN apt update && apt install -y procps && pip3 install kb-python==${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 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 gffutils
+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:
@@ -10,14 +17,64 @@ def validate_file(f):
         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")
+    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)
 
-  db = gffutils.create_db(args.gtf, dbfn = ":memory:", force = True, merge_strategy="merge", disable_infer_transcripts=True, disable_infer_genes=True)
-  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.write(str(transcript["transcript_id"][0]) + "\t" + str(gene["gene_id"][0]) + "\n")

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
 

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 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 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 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
 

src/.docker_modules/macs3/3.0.0a6/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/macs3:3.0.0a6
-docker build src/.docker_modules/macs3/3.0.0a6 -t 'lbmc/macs3:3.0.0a6'
-docker push lbmc/macs3:3.0.0a6
+# docker build src/.docker_modules/macs3/3.0.0a6 -t 'lbmc/macs3:3.0.0a6'
+# docker push lbmc/macs3:3.0.0a6
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/macs3:3.0.0a6" --push src/.docker_modules/macs3/3.0.0a6

src/.docker_modules/minimap2/2.17/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools 
 # /usr/local/bin/samtools
 # / # ldd /usr/local/bin/samtools