Include samtools package in gwas.sif

Fixes #219

CHANGELOG.md

@@ -39,6 +39,12 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
+## [1.6.0] - 2023-10-20
+
+### Added
+
+* Added `samtools` to `gwas.sif` container
+
 ## [1.5.1] - 2023-10.20
 
 ### Fixed

docker/README.md

@@ -59,6 +59,7 @@ The detailed description of the available container [files](https://github.com/c
   | gwas.sif          | plink2_avx2         | v2.00a3.6LM AVX2 Intel (24 Jan 2020)      | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | PRSice_linux        | 2.3.3 (2020-08-05)                        | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | regenie             | v3.2.8                                    | [MIT/Boost](https://github.com/rgcgithub/regenie/blob/master/LICENSE)
+  | gwas.sif          | samtools            | v1.12                                     | [MIT/ExpatD](https://github.com/samtools/samtools/blob/develop/LICENSE)
   | gwas.sif          | shapeit4.2          | v4.2.2                                    | [MIT](https://opensource.org/licenses/MIT)
   | gwas.sif          | shapeit5 phase_rare | v5.1.1                                    | [MIT](https://opensource.org/licenses/MIT)
   | gwas.sif          | shapeit5 phase_common | v5.1.1                                  | [MIT](https://opensource.org/licenses/MIT)

docker/dockerfiles/gwas/Dockerfile

@@ -170,4 +170,11 @@ COPY /scripts/install_duohmm.sh /tmp/duohmm/
 RUN bash /tmp/duohmm/install_duohmm.sh && \
     rm -rf /tmp/duohmm
 
+
+# samtools
+WORKDIR /tmp/samtools
+COPY /scripts/install_samtools.sh /tmp/samtools/
+RUN bash /tmp/samtools/install_samtools.sh && \
+    rm -rf /tmp/samtools
+
 WORKDIR /tools

docker/scripts/apt_get_essential.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 set -euo pipefail
 
-apt-get update && apt-get install -y --no-install-recommends apt-utils=2.0.9
+apt-get update && apt-get install -y --no-install-recommends apt-utils=2.0.10
 apt-get update && apt-get install -y --no-install-recommends ca-certificates=20230311ubuntu0.20.04.1 && \
    update-ca-certificates
 
@@ -12,27 +12,27 @@ apt-get update && apt-get install -y --no-install-recommends \
    build-essential=12.8ubuntu1 \
    bzip2=1.0.8-2 \
    cmake=3.16.3-1ubuntu1.20.04.1 \
-   curl=7.68.0-1ubuntu2.19 \
+   curl=7.68.0-1ubuntu2.21 \
    dos2unix=7.4.0-2 \
    gfortran=4:9.3.0-1ubuntu2 \
    git=1:2.25.1-1ubuntu3.11 \
    less=551-1ubuntu0.1 \
    libatlas-base-dev=3.10.3-8ubuntu7 \
-   libcurl4-openssl-dev=7.68.0-1ubuntu2.19 \
+   libcurl4-openssl-dev=7.68.0-1ubuntu2.21 \
    libgomp1=10.5.0-1ubuntu1~20.04 \
-   libgsl-dev=2.5+dfsg-6build1 \
+   libgsl-dev=2.5+dfsg-6+deb10u1build0.20.04.1 \
    libnss3=2:3.49.1-1ubuntu1.9 \
    libpcre2-dev=10.34-7ubuntu0.1 \
    libxt-dev=1:1.1.5-1 \
    pandoc=2.5-3build2 \
    pandoc-citeproc=0.15.0.1-1build4 \
    parallel=20161222-1.1 \
-   perl=5.30.0-9ubuntu0.4 \
+   perl=5.30.0-9ubuntu0.5 \
    pkg-config=0.29.1-0ubuntu4 \
-   tar=1.30+dfsg-7ubuntu0.20.04.2 \
+   tar=1.30+dfsg-7ubuntu0.20.04.4 \
    tofrodos=1.7.13+ds-4 \
    unzip=6.0-25ubuntu1.1 \
-   vim=2:8.1.2269-1ubuntu5.17 \
+   vim=2:8.1.2269-1ubuntu5.21 \
    wget=1.20.3-1ubuntu2 \
    zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5 \
    && \

docker/scripts/install_samtools.sh

@@ -0,0 +1,11 @@
+#!/bin/sh
+set -euo pipefail
+
+# bcfools
+git clone --depth 1 -b 1.12 https://github.com/samtools/samtools.git && \
+cd bcftools && \
+    autoheader && \
+    autoconf -Wno-syntax && \
+    ./configure --with-htslib=/usr/ && \
+    make -j12 && \
+    make install

tests/test_gwas.py

@@ -151,6 +151,12 @@ def test_gwas_regenie():
     assert out.returncode == 0
 
 
+def test_gwas_samtools():
+    call = f'singularity run {pth} samtools --help'
+    out = subprocess.run(call.split(' '))
+    assert out.returncode == 0
+
+
 def test_gwas_shapeit4():
     call = f'singularity run {pth} shapeit4.2 --help'
     out = subprocess.run(call.split(' '))

version/version.py

@@ -1,8 +1,8 @@
 _MAJOR = "1"
-_MINOR = "5"
+_MINOR = "6"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "1"
+_PATCH = "0"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""