From e1e391b47fcd92cb3e6ec50a81389b57e3e6a54e Mon Sep 17 00:00:00 2001 From: Keiran Raine Date: Tue, 3 Feb 2015 13:09:43 +0000 Subject: [PATCH 1/2] Fixed conflict, removed duplicated line --- bin/caveman.pl | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/bin/caveman.pl b/bin/caveman.pl index 05558f7..a36001d 100755 --- a/bin/caveman.pl +++ b/bin/caveman.pl @@ -269,8 +269,8 @@ sub setup { 'st|seqType=s' => \$opts{'seqType'}, ) or pod2usage(2); - pod2usage(-message => PCAP::license, -verbose => 2) if(defined $opts{'h'}); - pod2usage(-message => PCAP::license, -verbose => 1) if(defined $opts{'m'}); + pod2usage(-message => PCAP::license, -verbose => 1) if(defined $opts{'h'}); + pod2usage(-message => PCAP::license, -verbose => 2) if(defined $opts{'m'}); # then check for no args: my $defined; @@ -453,7 +453,6 @@ =head1 SYNOPSIS -logs -g Location to write logs (default is ./logs) -normal-protocol -np Normal protocol [WGS|WXS|RNA] (default WGS) -tumour-protocol -tp Tumour protocol [WGS|WXS|RNA] (default WGS) - -threads -t Number of threads allowed on this machine (default 1) -tum-cn-default -td Default tumour CN to use with gaps or no file provided -norm-cn-default -nd Default normal CN to use with gaps or no file provided From af33d0ba28bb40ba406e6aa424aacc6451d02366 Mon Sep 17 00:00:00 2001 From: Keiran Raine Date: Tue, 3 Feb 2015 13:10:03 +0000 Subject: [PATCH 2/2] Updated to CaVEMan 1.5.2 --- setup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.sh b/setup.sh index cd8254c..027c499 100755 --- a/setup.sh +++ b/setup.sh @@ -21,7 +21,7 @@ # along with this program. If not, see . ##########LICENCE########## -CAVEMAN_CORE="https://github.com/cancerit/CaVEMan/archive/1.5.1.tar.gz" +CAVEMAN_CORE="https://github.com/cancerit/CaVEMan/archive/1.5.2.tar.gz" SOURCE_HTSLIB="https://github.com/samtools/htslib/archive/1.1.tar.gz" SOURCE_SAMTOOLS="https://github.com/samtools/samtools/archive/1.1.tar.gz"