Merge pull request #1 from cancerit/dev

Checked in interface for obvious ommisions

README.md

@@ -0,0 +1,58 @@
+LICENCE
+=======
+Copyright (c) 2014 Genome Research Ltd.
+
+Author: CancerIT <[email protected]>
+
+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 <http://www.gnu.org/licenses/>.
+
+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.

perl/bin/ascat_version.pl

@@ -1,5 +1,26 @@
 #!/usr/bin/perl
 
+##########LICENCE##########
+# Copyright (c) 2014 Genome Research Ltd.
+#
+# Author: CancerIT <[email protected]>
+#
+# 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 <http://www.gnu.org/licenses/>.
+##########LICENCE##########
+
 use strict;
 use Sanger::CGP::Ascat
 

setup.sh

@@ -1,5 +1,26 @@
 #!/bin/bash
 
+########## LICENCE ##########
+# Copyright (c) 2014 Genome Research Ltd.
+#
+# Author: CancerIT <[email protected]>
+#
+# 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 <http://www.gnu.org/licenses/>.
+########## 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