diff --git a/Changes b/Changes index 6c12ea3..2e6cf74 100644 --- a/Changes +++ b/Changes @@ -1,3 +1,8 @@ +1.0.0 + bam_stats.pl actually installed now. + Basic *.bas perl access module. + Upgraded libmaus/biobambam to resolve patch and CentOS install issue. + Reference implementations ensure unique RG:ID between files. 0.3.0 Changes for the re-worked PanCancer submission SOP. Patch for libmaus issue as not going to be a release in time. diff --git a/INSTALL b/INSTALL index bd4bd5c..03c46c9 100644 --- a/INSTALL +++ b/INSTALL @@ -14,14 +14,25 @@ OS: Other Software For installation to proceed you require the following packages: - zlib1g-dev - g++ - dh-autoreconf - libncurses-dev - pkg-config - libgd2-xpm-dev - - This listing is based on Ubuntu 12.04 + For Ubuntu (tested with 12.04) + apt-get + zlib1g-dev + g++ + dh-autoreconf + libncurses-dev + pkg-config + libgd2-xpm-dev + + For CentOS (tested with 6.4) + yum install + zlib-devel + gcc-c++ + autoconf + automake + libtool + boost-devel.x86_64 + ncurses-devel.x86_64 + gd-devel setup.sh will install biobambam diff --git a/MANIFEST b/MANIFEST index a14d4d2..6757b7b 100644 --- a/MANIFEST +++ b/MANIFEST @@ -21,7 +21,6 @@ LICENSE Makefile.PL MANIFEST This list of files MANIFEST.SKIP -patches/fileModeFix.diff prerelease.sh README.md setup.sh diff --git a/MYMETA.json b/MYMETA.json index 490d11e..d70d5dc 100644 --- a/MYMETA.json +++ b/MYMETA.json @@ -53,5 +53,5 @@ } }, "release_status" : "stable", - "version" : "v0.3.0" + "version" : "v1.0.0" } diff --git a/MYMETA.yml b/MYMETA.yml index b32d144..d132837 100644 --- a/MYMETA.yml +++ b/MYMETA.yml @@ -35,4 +35,4 @@ requires: Term::UI: 0.42 Test::Fatal: 0.013 Try::Tiny: 0.19 -version: v0.3.0 +version: v1.0.0 diff --git a/docs.tar.gz b/docs.tar.gz index 71b6e18..c6ef546 100644 Binary files a/docs.tar.gz and b/docs.tar.gz differ diff --git a/lib/PCAP.pm b/lib/PCAP.pm index 124649a..9f4eab2 100644 --- a/lib/PCAP.pm +++ b/lib/PCAP.pm @@ -23,7 +23,7 @@ package PCAP; use strict; use Const::Fast qw(const); -our $VERSION = '0.3.0'; +our $VERSION = '1.0.0'; const my $LICENSE => "################# @@ -33,11 +33,13 @@ const my $LICENSE => #################"; const my $DEFAULT_PATH => 'biobambam,samtools,bwa'; -const my %UPGRADE_PATH => ( '0.1.0' => 'biobambam,samtools,bwa', - '0.1.1' => 'biobambam,bwa', - '0.1.2' => 'biobambam', - '0.2.0' => 'biobambam', - '0.3.0' => '', +const my %UPGRADE_PATH => ( '0.1.0' => 'biobambam,samtools,bwa', + '0.1.1' => 'biobambam,bwa', + '0.1.2' => 'biobambam', + '0.2.0' => 'biobambam', + '0.2.99' => 'biobambam', + '0.3.0' => 'biobambam', + '1.0.0' => '', ); sub license {