src/.docker_modules/tinycov/0.3.1/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 TINYCOV_VERSION=0.3.1
+
+RUN apt update \
+ && apt install -y  procps \
+ && pip install tinycov==$TINYCOV_VERSION 
+
+
+CMD ["bash"]

src/.docker_modules/tinycov/0.3.1/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/tinycov:0.3.1
+docker build src/.docker_modules/tinycov/0.3.1 -t 'lbmc/tinycov:0.3.1'
+docker push lbmc/tinycov:0.3.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/tinycov:0.3.1" --push src/.docker_modules/tinycov/0.3.1

src/.docker_modules/tophat/2.1.1/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 TOPHAT_VERSION=2.1.1
+ENV PACKAGES tophat=${TOPHAT_VERSION}*\
+             bowtie=1.2.2*\
+             libsys-hostname-long-perl
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES}  && \
+    apt-get clean

src/.docker_modules/tophat/2.1.1/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/tophat:2.1.1
+# docker build src/.docker_modules/tophat/2.1.1 -t 'lbmc/tophat:2.1.1'
+# docker push lbmc/tophat:2.1.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/tophat:2.1.1" --push src/.docker_modules/tophat/2.1.1

src/docker_modules/Trimmomatic/0.36/Dockerfile → src/.docker_modules/trimmomatic/0.36/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/trimmomatic/0.36/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/trimmomatic:0.36
+# docker build src/.docker_modules/trimmomatic/0.36 -t 'lbmc/trimmomatic:0.36'
+# docker push lbmc/trimmomatic:0.36
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/trimmomatic:0.36" --push src/.docker_modules/trimmomatic/0.36

src/.docker_modules/trinity/2.13.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/trinity:2.13.2--ha140323_0
+
+ENV TRINITY_VERSION=2.13.2--ha140323_0

src/.docker_modules/trinity/2.13.2/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/trinity:2.13.2
+docker build src/.docker_modules/trinity/2.13.2 -t 'lbmc/trinity:2.13.2'
+docker push lbmc/trinity:2.13.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/trinity:2.13.2" --push src/.docker_modules/trinity/2.13.2

src/.docker_modules/ucsc/375/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:jessie
+MAINTAINER Laurent Modolo
+
+ENV PACKAGES apt-utils \
+             curl \
+             build-essential \
+             libssl-dev \
+             libpng-dev \
+             uuid-dev \
+             libmysqlclient-dev \
+             procps \
+             rsync
+
+
+RUN apt-get update && \
+    apt-get install -y ${PACKAGES}
+
+ENV UCSC_VERSION=375
+
+RUN curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
+tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
+cd userApps/ && \
+make &&\
+cd .. &&\
+mv userApps/bin/* /usr/bin/ &&\
+rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
+rm -R userApps

src/.docker_modules/ucsc/375/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/ucsc:375
+# docker build src/.docker_modules/ucsc/375/ -t 'lbmc/ucsc:375'
+# docker push lbmc/ucsc:375
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/ucsc:375" --push src/.docker_modules/ucsc/375

src/.docker_modules/ucsc/400/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:jessie
+MAINTAINER Laurent Modolo
+
+ENV PACKAGES apt-utils \
+             curl \
+             build-essential \
+             libssl-dev \
+             libpng-dev \
+             uuid-dev \
+             libmysqlclient-dev \
+             procps \
+             rsync
+
+
+RUN apt-get update && \
+    apt-get install -y ${PACKAGES}
+
+ENV UCSC_VERSION=400
+
+RUN curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
+tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
+cd userApps/ && \
+make &&\
+cd .. &&\
+mv userApps/bin/* /usr/bin/ &&\
+rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
+rm -R userApps

src/.docker_modules/ucsc/400/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/ucsc:400
+# docker build src/.docker_modules/ucsc/400/ -t 'lbmc/ucsc:400'
+# docker push lbmc/ucsc:400
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/ucsc:400" --push src/.docker_modules/ucsc/400

src/.docker_modules/ucsc/407/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:jessie
+MAINTAINER Laurent Modolo
+
+ENV PACKAGES apt-utils \
+             curl \
+             build-essential \
+             libssl-dev \
+             libpng-dev \
+             uuid-dev \
+             libmysqlclient-dev \
+             procps \
+             rsync
+
+
+RUN apt-get update && \
+    apt-get install -y ${PACKAGES}
+
+ENV UCSC_VERSION=407
+
+RUN curl -k -L http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v${UCSC_VERSION}.src.tgz -o userApps.v${UCSC_VERSION}.src.tgz &&\
+tar xvf userApps.v${UCSC_VERSION}.src.tgz &&\
+cd userApps/ && \
+make &&\
+cd .. &&\
+mv userApps/bin/* /usr/bin/ &&\
+rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
+rm -R userApps
+
+COPY bedgraph_to_wig.pl /usr/bin/
+COPY gtf2bed.pl /usr/bin/
+RUN chmod +x /usr/bin/*.pl
\ No newline at end of file

src/.docker_modules/ucsc/407/bedgraph_to_wig.pl

+#!/usr/bin/perl
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+# Description: This script converts bedGraph to fixedStep wig format with defined step size. Input file may be compressed as .gz.
+# Coordinates in bedGraph input are assumed to be 0-based (http://genome.ucsc.edu/goldenPath/help/bedgraph.html).
+# Coordinates in wig output are 1-based (http://genome.ucsc.edu/goldenPath/help/wiggle.html). 
+
+# Usage: bedgraph_to_wig.pl --bedgraph input.bedgraph --wig output.wig --step step_size [--compact]
+# --bedgraph : specify input file in bedGraph format.
+# --wig : specify output file in fixedStep format.
+# --step : specify step size. Note that span is set to be identical to step.
+# --compact : if selected, steps with value equal to 0 will not be printed. This saves space but was not allowed in original wig format, thus some scripts using wig file as input may not understand it.
+
+# Credits: This script was written by Sebastien Vigneau (sebastien.vigneau@gmail.com) in Alexander Gimelbrant lab (Dana-Farber Cancer Institute). The inspiration for this script comes from Dave Tang's own version (http://davetang.org/wiki/tiki-index.php?page=wig).
+
+
+use strict;
+use warnings;
+use Getopt::Long;
+use List::Util qw[min max];
+
+my $usage = "Usage: $0 --bedgraph <infile.bedgraph> --wig <outfile.wig> --step <step_size> [--compact]\n";
+
+# Parse command line arguments
+
+my $infile; # bedGraph input file name
+my $outfile; # wig output file name
+my $step; # wig step size
+my $compact; # if selected, steps with value equal to 0 will not be printed
+
+GetOptions (
+  "bedgraph=s" => \$infile,
+  "wig=s" => \$outfile,
+  "step=i" => \$step,
+  "compact" => \$compact,
+) or die ("Error in command line arguments!\n$usage\n");
+
+# Open input file. If it is compressed with gunzip, uncompress it.
+
+if ($infile =~ /\.gz$/){
+  open(IN,'-|',"gunzip -c $infile") || die "Could not open $infile: $!\n";
+} else {
+  open(IN,'<',$infile) || die "Could not open $infile: $!\n";
+}
+
+# Open output file.
+
+open(OUT,'>',$outfile) || die "Could not open $outfile: $!\n";
+
+
+# bedGraph to wig conversion starts here.
+
+# Print main header.
+
+print OUT "track type=wiggle_0 name=\"$infile\" description=\"$infile\" visibility=full\n";
+
+# Initialize variables.
+
+my $cur_chr = 0; # chromosome being processed
+my $cur_pos = 0; # position of current step
+my $next_pos = $cur_pos + $step; # position of next step
+my $exp_pos = 0; # expected position if no step was skipped; used with --compact option
+my $cur_val = 0; # value for current step
+
+while (<IN>) {
+
+  chomp;
+
+  # Skip comment lines
+  next if (/^track/);
+  next if (/^#/);
+
+  # Parse relevant information in current line 
+  # e.g: chr1 3000400 3000500 2
+  my ($chr, $start, $end, $val) = split(/\t/);
+  
+  # Print header for new chromosome and initialize variables.
+  if ($chr ne $cur_chr) {
+    $cur_chr = $chr;
+    $cur_pos = 0;
+    $next_pos = $cur_pos + $step;
+    $cur_val = 0;
+    if (!$compact) { # If --compact option selected, header will be printed immediately before non-null value.
+      print OUT "fixedStep chrom=$chr start=", $cur_pos + 1, " step=$step span=$step\n";
+      # +1 was added to convert from 0-based to 1-based coordinates.
+    }
+  }
+  
+  # Print values when gap in bedGraph file is greater than step.
+  while ($start >= $next_pos) {
+    print_wig_line($cur_chr, \$cur_pos, \$next_pos, \$exp_pos, \$cur_val, $chr, $start, $end, $val, $step);
+  }
+  
+  # Print values when step overlaps with bedGraph interval and bedGraph interval is longer than step.
+  while ($end >= $next_pos) {
+    $cur_val += $val * ($next_pos - max($cur_pos, $start));
+    print_wig_line($cur_chr, \$cur_pos, \$next_pos, \$exp_pos, \$cur_val, $chr, $start, $end, $val, $step);
+  }
+
+  # Update value when end of bedGraph interval is contained within step.
+  if ($end < $next_pos) {
+    $cur_val += $val * ($end - max($cur_pos, $start));
+  }
+
+}
+
+close(IN);
+close(OUT);
+
+exit(0);
+
+
+# Print or skip line in wig file depending on --compact option and value; update variables for next step.
+sub print_wig_line {
+  my ($cur_chr, $cur_pos, $next_pos, $exp_pos, $cur_val, $chr, $start, $end, $val, $step) = @_;
+  if (!$compact) { # Always print if --compact option was not selected.
+    my $cur_ave_val = $$cur_val / $step;
+    print OUT "$cur_ave_val\n";
+  } elsif ($$cur_val != 0) { # Skips printing if --compact option selected and value is null.
+    if ($$cur_pos == 0 || $$cur_pos != $$exp_pos) {
+      # Adds header if first step in chromosome, or if previous step had null value and was skipped in print out.
+      print OUT "fixedStep chrom=$chr start=", $$cur_pos + 1, " step=$step span=$step\n";
+      # +1 was added to convert from 0-based to 1-based coordinates.
+    }
+    my $cur_ave_val = $$cur_val / $step;
+    print OUT "$cur_ave_val\n";
+    $$exp_pos = $$next_pos;
+  }
+  $$cur_pos = $$next_pos;
+  $$next_pos = $$cur_pos + $step;
+  $$cur_val = 0;
+}

src/.docker_modules/ucsc/407/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/ucsc:407
+# docker build src/.docker_modules/ucsc/407/ -t 'lbmc/ucsc:407'
+# docker push lbmc/ucsc:407
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/ucsc:407" --push src/.docker_modules/ucsc/407

src/.docker_modules/ucsc/407/gtf2bed.pl

+#!/usr/bin/perl
+
+# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+use Getopt::Long;
+
+my $extended;
+GetOptions("x"=>\$extended);
+
+$in = shift @ARGV;
+
+my $in_cmd =($in =~ /\.gz$/ ? "gunzip -c $in|" : $in =~ /\.zip$/ ? "unzip -p $in|" : "$in") || die "Can't open $in: $!\n";
+open IN, $in_cmd;
+
+while (<IN>) {
+	$gff = 2 if /^##gff-version 2/;
+	$gff = 3 if /^##gff-version 3/;
+	next if /^#/ && $gff;
+
+	s/\s+$//;
+	# 0-chr 1-src 2-feat 3-beg 4-end 5-scor 6-dir 7-fram 8-attr
+	my @f = split /\t/;
+	if ($gff) {
+        # most ver 2's stick gene names in the id field
+		($id) = $f[8]=~ /\bID="([^"]+)"/;
+        # most ver 3's stick unquoted names in the name field
+		($id) = $f[8]=~ /\bName=([^";]+)/ if !$id && $gff == 3;
+	} else {
+		($id) = $f[8]=~ /transcript_id "([^"]+)"/;
+	}
+
+	next unless $id && $f[0];
+
+	if ($f[2] eq 'exon') {
+		die "no position at exon on line $." if ! $f[3];
+        # gff3 puts :\d in exons sometimes
+        $id =~ s/:\d+$// if $gff == 3;
+		push @{$exons{$id}}, \@f;
+		# save lowest start
+		$trans{$id} = \@f if !$trans{$id};
+	} elsif ($f[2] eq 'start_codon') {
+		#optional, output codon start/stop as "thick" region in bed
+		$sc{$id}->[0] = $f[3];
+	} elsif ($f[2] eq 'stop_codon') {
+		$sc{$id}->[1] = $f[4];
+	} elsif ($f[2] eq 'miRNA' ) {
+		$trans{$id} = \@f if !$trans{$id};
+		push @{$exons{$id}}, \@f;
+	}
+}
+
+for $id (
+	# sort by chr then pos
+	sort {
+		$trans{$a}->[0] eq $trans{$b}->[0] ?
+		$trans{$a}->[3] <=> $trans{$b}->[3] :
+		$trans{$a}->[0] cmp $trans{$b}->[0]
+	} (keys(%trans)) ) {
+		my ($chr, undef, undef, undef, undef, undef, $dir, undef, $attr, undef, $cds, $cde) = @{$trans{$id}};
+        my ($cds, $cde);
+        ($cds, $cde) = @{$sc{$id}} if $sc{$id};
+
+		# sort by pos
+		my @ex = sort {
+			$a->[3] <=> $b->[3]
+		} @{$exons{$id}};
+
+		my $beg = $ex[0][3];
+		my $end = $ex[-1][4];
+		
+		if ($dir eq '-') {
+			# swap
+			$tmp=$cds;
+			$cds=$cde;
+			$cde=$tmp;
+			$cds -= 2 if $cds;
+			$cde += 2 if $cde;
+		}
+
+		# not specified, just use exons
+		$cds = $beg if !$cds;
+		$cde = $end if !$cde;
+
+		# adjust start for bed
+		--$beg; --$cds;
+	
+		my $exn = @ex;												# exon count
+		my $exst = join ",", map {$_->[3]-$beg-1} @ex;				# exon start
+		my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex;			# exon size
+
+        my $gene_id;
+        my $extend = "";
+        if ($extended) {
+    	    ($gene_id) = $attr =~ /gene_name "([^"]+)"/;
+    	    ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id;
+            $extend="\t$gene_id";
+        }
+		# added an extra comma to make it look exactly like ucsc's beds
+		print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+}
+
+
+close IN;
+

src/.docker_modules/umi_tools/0.5.4/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/umi_tools:0.5.4--py27hdd9f355_1
+MAINTAINER Rémi SERAPHIN

src/.docker_modules/umi_tools/0.5.4/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/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

src/.docker_modules/umi_tools/1.0.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:stretch
+MAINTAINER Rémi SERAPHIN
+
+ENV UMI_TOOLS_VERSION=1.0.0
+ENV PACKAGES="bash \
+              python3 \
+              python3-dev \
+              python3-pip \
+              procps \
+              zlib1g-dev \
+              zlib1g \
+              bzip2 \
+              libbz2-dev \
+              liblzma-dev \
+              libcurl4-openssl-dev \
+              make \t 
+              gcc"
+
+RUN apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+RUN pip3 install setuptools
+RUN pip3 install umi_tools==${UMI_TOOLS_VERSION}
+

src/.docker_modules/umi_tools/1.0.0/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/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