From edfe6d6d02a8002c6f2cf2624e238d48e11be833 Mon Sep 17 00:00:00 2001 From: Keiran Raine Date: Wed, 23 Sep 2020 10:40:13 +0000 Subject: [PATCH 1/4] Version bumps to get new samtools into stack --- CHANGES.md | 6 ++++++ Dockerfile | 6 +++--- lib/PCAP.pm | 2 +- setup.sh | 4 ++-- 4 files changed, 12 insertions(+), 6 deletions(-) diff --git a/CHANGES.md b/CHANGES.md index ac2660b..1332074 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,5 +1,11 @@ # CHANGES +## 5.4.0 + +* Update base image of docker to cgpbigwig 1.5.0 +* Update to htslib 1.11 +* Update to samtools 1.11 - to handle long running markdup issue + ## 5.3.0 * Support for paired FASTQ names ending with `_R1_001` and `_R2_001` in addition to `_1` and `_2` as before. diff --git a/Dockerfile b/Dockerfile index b28ee09..1717f80 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM quay.io/wtsicgp/cgpbigwig:1.3.0 as builder +FROM quay.io/wtsicgp/cgpbigwig:1.5.0 as builder USER root @@ -11,8 +11,8 @@ ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2 ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz" ARG VER_BIODBHTS="3.01" ARG VER_BWA="v0.7.17" -ARG VER_HTSLIB="1.10.2" -ARG VER_SAMTOOLS="1.10" +ARG VER_HTSLIB="1.11" +ARG VER_SAMTOOLS="1.11" RUN apt-get -yq update RUN apt-get install -yq --no-install-recommends apt-transport-https diff --git a/lib/PCAP.pm b/lib/PCAP.pm index d53ebb0..a739938 100644 --- a/lib/PCAP.pm +++ b/lib/PCAP.pm @@ -28,7 +28,7 @@ use FindBin qw($Bin); use File::Which qw(which); # don't use autodie, only core perl in here -our $VERSION = '5.3.0'; +our $VERSION = '5.4.0'; our @EXPORT = qw($VERSION _which); const my $LICENSE => diff --git a/setup.sh b/setup.sh index e01195d..040df21 100755 --- a/setup.sh +++ b/setup.sh @@ -9,8 +9,8 @@ export BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0p export STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz" export VER_BIODBHTS="3.01" export VER_BWA="v0.7.17" -export VER_HTSLIB="1.10.2" -export VER_SAMTOOLS="1.10" +export VER_HTSLIB="1.11" +export VER_SAMTOOLS="1.11" if [[ ($# -ne 1 && $# -ne 2) ]] ; then From 5fcc17fceda0cc7ec3160d3b23369ae661e2094b Mon Sep 17 00:00:00 2001 From: Keiran Raine Date: Wed, 23 Sep 2020 10:59:21 +0000 Subject: [PATCH 2/4] don't update htslib for BIO::DB::HTS --- Dockerfile | 3 ++- setup.sh | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1717f80..72b8ffa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,8 +11,9 @@ ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2 ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz" ARG VER_BIODBHTS="3.01" ARG VER_BWA="v0.7.17" -ARG VER_HTSLIB="1.11" ARG VER_SAMTOOLS="1.11" +# only used for Bio::DB::HTS, tests fail with 1.11 +ARG VER_HTSLIB="1.10.2" RUN apt-get -yq update RUN apt-get install -yq --no-install-recommends apt-transport-https diff --git a/setup.sh b/setup.sh index 040df21..debe790 100755 --- a/setup.sh +++ b/setup.sh @@ -9,8 +9,9 @@ export BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0p export STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz" export VER_BIODBHTS="3.01" export VER_BWA="v0.7.17" -export VER_HTSLIB="1.11" export VER_SAMTOOLS="1.11" +# only used for Bio::DB::HTS, tests fail with 1.11 +export VER_HTSLIB="1.10.2" if [[ ($# -ne 1 && $# -ne 2) ]] ; then From 7b25d323eaad06a3da3072f10a6f7f1c4c0375dd Mon Sep 17 00:00:00 2001 From: Keiran Raine Date: Wed, 23 Sep 2020 11:33:23 +0000 Subject: [PATCH 3/4] Update tests to use definitions available from htslib --- Dockerfile | 3 +-- c/c_tests/02_bam_access_tests.c | 31 ------------------------------- setup.sh | 3 +-- 3 files changed, 2 insertions(+), 35 deletions(-) diff --git a/Dockerfile b/Dockerfile index 72b8ffa..1717f80 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,9 +11,8 @@ ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2 ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz" ARG VER_BIODBHTS="3.01" ARG VER_BWA="v0.7.17" +ARG VER_HTSLIB="1.11" ARG VER_SAMTOOLS="1.11" -# only used for Bio::DB::HTS, tests fail with 1.11 -ARG VER_HTSLIB="1.10.2" RUN apt-get -yq update RUN apt-get install -yq --no-install-recommends apt-transport-https diff --git a/c/c_tests/02_bam_access_tests.c b/c/c_tests/02_bam_access_tests.c index cd57b0b..85a4139 100644 --- a/c/c_tests/02_bam_access_tests.c +++ b/c/c_tests/02_bam_access_tests.c @@ -21,37 +21,6 @@ #include "minunit.h" #include "bam_access.h" -#ifndef KSTRING_T -#define KSTRING_T kstring_t -typedef struct __kstring_t { - size_t l, m; - char *s; -} kstring_t; -#endif - -static inline int kputsn(const char *p, int l, kstring_t *s) -{ - if (s->l + l + 1 >= s->m) { - s->m = s->l + l + 2; - kroundup32(s->m); - s->s = (char*)realloc(s->s, s->m); - } - memcpy(s->s + s->l, p, l); - s->l += l; - s->s[s->l] = 0; - return l; -} - - -static inline int kputs(const char *p, kstring_t *s) -{ - return kputsn(p, strlen(p), s); -} - -#ifndef kroundup32 -#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) -#endif - char *test_bam = "../t/data/Stats.bam"; char *exp_plat = "GAII"; char *exp_sample = "PD1234a"; diff --git a/setup.sh b/setup.sh index debe790..040df21 100755 --- a/setup.sh +++ b/setup.sh @@ -9,9 +9,8 @@ export BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0p export STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz" export VER_BIODBHTS="3.01" export VER_BWA="v0.7.17" +export VER_HTSLIB="1.11" export VER_SAMTOOLS="1.11" -# only used for Bio::DB::HTS, tests fail with 1.11 -export VER_HTSLIB="1.10.2" if [[ ($# -ne 1 && $# -ne 2) ]] ; then From 14455469970950cae3233a3fcfa5fa5152b157e7 Mon Sep 17 00:00:00 2001 From: Keiran Raine Date: Wed, 23 Sep 2020 15:33:27 +0000 Subject: [PATCH 4/4] update version in dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1717f80..3a98daf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -62,7 +62,7 @@ FROM ubuntu:20.04 LABEL maintainer="cgphelp@sanger.ac.uk"\ uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \ - version="5.3.0" \ + version="5.4.0" \ description="pcap-core" ENV OPT /opt/wtsi-cgp