Commit 334fed2c authored by Blaise Li's avatar Blaise Li
Browse files

Adding licence.

parent e7edabf0
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
Snakefile to process iCLIP data.
"""
......
#!/usr/bin/env bash
# Usage: iCLIP_trim_and_dedup.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmed_nodedup> <trimmer log> <nb_raw> <nb_adapt> <nb_adapt_deduped> <nb_noadapt> <nb_noadapt_deduped>
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# http://linuxcommand.org/wss0150.php
PROGNAME=$(basename $0)
......
gpl.txt
\ No newline at end of file
COPYING.txt
\ No newline at end of file
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
Snakefile to analyse Degradome-seq data.
"""
......
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
Snakefile to analyse PRO-seq data.
"""
......
#!/usr/bin/env bash
# Usage: PRO-seq_trim_and_dedup.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmer log> <nb_raw> <nb_adapt> <nb_adapt_deduped> <nb_noadapt> <nb_noadapt_deduped>
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# http://linuxcommand.org/wss0150.php
PROGNAME=$(basename $0)
......
#!/usr/bin/env bash
# Usage: PRO-seq_trim_only.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmer log> <nb_raw> <nb_adapt> <nb_noadapt>
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# http://linuxcommand.org/wss0150.php
PROGNAME=$(basename $0)
......
#!/usr/bin/env Rscript
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
options(show.error.locations=TRUE)
# Trying to automatically install docopt
......
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
Snakefile to analyse RNA-seq data.
"""
......
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
Snakefile to analyse small_RNA-seq data.
......
bam25prime @ 508be30b
Subproject commit b54d1ca837f41e1b8eaf1b7984d4799ca2cc50e4
Subproject commit 508be30bc5d719779ad47c0ecc5af06ac890b6df
libcelegans @ 48afc688
Subproject commit 36938bcfd6c1e4d1b51ec39d7706fb17e08a64d4
Subproject commit 48afc688faabfee8a9b5ee75b183d93cb8238e12
libdeseq @ 196ee3d1
Subproject commit c4928c62ba6875dbe83e77caceb7265a7a81045d
Subproject commit 196ee3d15a125fad0d821256cc69f96c9129bf61
libhts @ 4441fea3
Subproject commit c4715fde8bf617a87906d9349432b2beb9462a43
Subproject commit 4441fea365110ca842eaea5fc5ae69a26765896e
libsmallrna @ b44e5256
Subproject commit 89178795d9dd148b1780a490b70c705b58a64b12
Subproject commit b44e5256fd5d42a63c8f0a6765e0d6af829d753d
libworkflows @ f38327c2
Subproject commit 4b3859c4c852c518b18d809954b60d8ce00c5d15
Subproject commit f38327c25d197c04da485d8691a463f10bc10fd4
plotting_scripts @ 03c60f76
Subproject commit 6a7e11405991a4fb273f40e03c5b7c02d1d52faa
Subproject commit 03c60f765ee1c9694b93638bae2293539e2cd3c5
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
Bootstrap:localimage
From:workflows_base.sif
......@@ -37,6 +51,9 @@ From:workflows_base.sif
"--version" | "-v")
exec cat /usr/local/share/doc/program_versions.txt
;;
"--licence")
exec cat /usr/local/src/bioinfo_utils/COPYING.txt
;;
"--help" | "-h")
exec echo "Usage: run_<seq_type>_pipeline <config.yaml> [<snakemake options> ...]"
;;
......
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
Bootstrap:docker
From:debian:buster-slim
Stage: build-haskell
......@@ -95,6 +109,7 @@ From:python:3.7-buster
prog="bedGraphToBigWig"
echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
# `|| :` is to "ignore" error exit code from bedGraphToBigWig
# TODO: fix this
eval "${prog}" 2>&1 | head -1 >> /usr/local/share/doc/program_versions.txt || :
# It is possible to test whether the R install is already OK
deb_source="deb http://cran.irsn.fr/bin/linux/debian buster-cran35/"
......
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