diff --git a/README b/README deleted file mode 100644 index e69de29..0000000 diff --git a/README.md b/README.md new file mode 100644 index 0000000..1c4574f --- /dev/null +++ b/README.md @@ -0,0 +1,58 @@ +LICENCE +======= +Copyright (c) 2014 Genome Research Ltd. + +Author: CancerIT + +This file is part of AscatNGS. + +AscatNGS is free software: you can redistribute it and/or modify it under +the terms of the GNU Affero 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 Affero General Public License for more +details. + +You should have received a copy of the GNU Affero General Public License +along with this program. If not, see . + +AscatNGS +======== +AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number +algorithm for paired end sequencing. + +For details of the underlying algorithm please see the [ASCAT](http://heim.ifi.uio.no/bioinf/Projects/ASCAT/) site. + +--- + +###Dependencies/Install +Please install the following first: + +* [PCAP-core](http://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases) +* [alleleCount](https://github.com/cancerit/alleleCount/releases) + +Please see these for any child dependencies. + +Once complete please run: + +./setup.sh /some/install/location + +Please be aware that this software requires the Rscript executable to be pre-installed. + +--- + +##Creating a release +####Preparation +* Commit/push all relevant changes. +* Pull a clean version of the repo and use this for the following steps. + +####Cutting the release +1. Update `perl/lib/Sanger/CGP/Ascat.pm` to the correct version (adding rc/beta to end if applicable). +2. Run `./prerelease.sh` +3. Check all tests and coverage reports are acceptable. +4. Commit the updated docs tree and updated module/version. +5. Push commits. +6. Use the GitHub tools to draft a release. diff --git a/perl/bin/ascat_version.pl b/perl/bin/ascat_version.pl index 43d2773..b65b60d 100755 --- a/perl/bin/ascat_version.pl +++ b/perl/bin/ascat_version.pl @@ -1,5 +1,26 @@ #!/usr/bin/perl +##########LICENCE########## +# Copyright (c) 2014 Genome Research Ltd. +# +# Author: CancerIT +# +# This file is part of AscatNGS. +# +# AscatNGS is free software: you can redistribute it and/or modify it under +# the terms of the GNU Affero 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 Affero General Public License for more +# details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . +##########LICENCE########## + use strict; use Sanger::CGP::Ascat diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz index b03393d..c82a586 100644 Binary files a/perl/docs.tar.gz and b/perl/docs.tar.gz differ diff --git a/setup.sh b/setup.sh index 6e9df8f..bdbd301 100755 --- a/setup.sh +++ b/setup.sh @@ -1,5 +1,26 @@ #!/bin/bash +########## LICENCE ########## +# Copyright (c) 2014 Genome Research Ltd. +# +# Author: CancerIT +# +# This file is part of AscatNGS. +# +# AscatNGS is free software: you can redistribute it and/or modify it under +# the terms of the GNU Affero 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 Affero General Public License for more +# details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . +########## LICENCE ########## + done_message () { if [ $? -eq 0 ]; then echo " done." @@ -63,6 +84,13 @@ if [[ "x$PCAP" == "x" ]] ; then exit 1; fi +AC=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::AlleleCount` +if [[ "x$AC" == "x" ]] ; then + echo "PREREQUISITE: Please install alleleCount before proceeding:" + echo " https://github.com/cancerit/alleleCount/releases" + exit 1; +fi + perlmods=( "File::ShareDir" "File::ShareDir::Install" ) set -e