Add/update requested gwas.sif binaries (#214)

* add gdb, ldak, snptest; update metal, qctool

* update changelog

* fixed tests

* updated changelog

* rebuilt gwas.sif

CHANGELOG.md

@@ -39,7 +39,20 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
-## [1.5.1] - 2023-10.20
+## [1.6.0] - 2023-12-12
+
+### Added
+
+- Added `gdb` debugger, `ldak` and `snptest` binaries to `gwas.sif` container
+- Added tests for `ldak` and `snptest` binaries in `gwas.sif` container
+
+### Updated
+
+- updated `metal` to version `2020-05-05` in `gwas.sif`
+- updated `qctool` to `v2.2.2` and added related binaries `inthinnerator`, `hptest`, `ldbird` and `selfmap` to `gwas.sif`
+- rebuilt `gwas.sif` (md5 checksum b6104b58d21f862f9d61a86d9d4802a6)
+
+## [1.5.1] - 2023-10-20
 
 ### Fixed
 

docker/README.md

@@ -48,11 +48,12 @@ The detailed description of the available container [files](https://github.com/c
   | gwas.sif          | flashpca_x86-64     | 2.0                                       | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | gcta64              | version 1.93.3 beta 2 Linux               | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | gctb                | 2.02                                      | [MIT](https://opensource.org/licenses/MIT)
-  | gwas.sif          | qctool              | 2.0.6, revision 18b8f17                   | [Boost](https://www.boost.org/LICENSE_1_0.txt)
+  | gwas.sif          | qctool              | 2.2.2, revision e5723df2c0c85959          | [Boost](https://www.boost.org/LICENSE_1_0.txt)
   | gwas.sif          | GWAMA               | 2.2.2                                     | [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause)
   | gwas.sif          | HTSlib              | 1.12                                      | [MIT/Expat/Modified-BSD](https://github.com/samtools/htslib/blob/develop/LICENSE)
   | gwas.sif          | king                | 2.2.9 - (c)                               | [permissive](https://www.kingrelatedness.com/Download.shtml)
-  | gwas.sif          | metal               | version released on 2011-03-25            | -
+  | gwas.sif          | ldak                | 5.2                                       | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | gwas.sif          | metal               | 2020-05-05                                | -
   | gwas.sif          | minimac4            | v4.1.0                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | plink               | v1.90b6.18 64-bit (16 Jun 2020)           | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | plink2              | v2.00a3.6LM 64-bit Intel (14 Aug 2022)    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
@@ -66,6 +67,7 @@ The detailed description of the available container [files](https://github.com/c
   | gwas.sif          | shapeit5 switch     | v5.1.1                                    | [MIT](https://opensource.org/licenses/MIT)
   | gwas.sif          | shapeit5 xcftools   | v5.1.1                                    | [MIT](https://opensource.org/licenses/MIT)
   | gwas.sif          | simu_linux          | v0.9.4                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | gwas.sif          | snptest             | v2.5.6                                    | [permissive](https://www.chg.ox.ac.uk/~gav/snptest/#download)
   | gwas.sif          | switchError         | 6e688b1                                   | [MIT](https://opensource.org/licenses/MIT)
   | gwas.sif          | vcftools            | 0.1.17                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | python3.sif       | ubuntu              | 20.04 (LTS)                               | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)

docker/dockerfiles/gwas/Dockerfile

@@ -59,18 +59,30 @@ COPY /scripts/install_gctb.sh /tmp/gctb/
 RUN bash /tmp/gctb/install_gctb.sh && \
     rm -rf /tmp/gctb
 
-# qctools
-WORKDIR /tmp/qctools
-COPY /scripts/install_qctools.sh /tmp/qctools/
-RUN bash /tmp/qctools/install_qctools.sh && \
-    rm -rf /tmp/qctools
+# qctool
+WORKDIR /tmp/qctool
+COPY /scripts/install_qctools.sh /tmp/qctool/
+RUN bash /tmp/qctool/install_qctools.sh && \
+    rm -rf /tmp/qctool
+
+# snptest
+WORKDIR /tmp/snptest
+COPY /scripts/install_snptest.sh /tmp/snptest/
+RUN bash /tmp/snptest/install_snptest.sh && \
+    rm -rf /tmp/snptest
 
 # king
 WORKDIR /tmp/king
 COPY /scripts/install_king.sh /tmp/king/
 RUN bash /tmp/king/install_king.sh && \
     rm -rf /tmp/king
 
+# ldak
+WORKDIR /tmp/ldak
+COPY /scripts/install_ldak.sh /tmp/ldak/
+RUN bash /tmp/ldak/install_ldak.sh && \
+    rm -rf /tmp/ldak
+
 # metal
 WORKDIR /tmp/metal
 COPY /scripts/install_metal.sh /tmp/metal/

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 +12,28 @@ 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 \
+   gdb=9.1-0ubuntu1 \
    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=2:8.1.2269-1ubuntu5.20 \
    wget=1.20.3-1ubuntu2 \
    zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5 \
    && \

docker/scripts/install_bcftools.sh

@@ -3,8 +3,8 @@ set -euo pipefail
 
 # deps 
 apt-get update && apt-get install -y --no-install-recommends \
-    libcurl4-gnutls-dev=7.68.0-1ubuntu2.19 \
-    libperl-dev=5.30.0-9ubuntu0.4 \
+    libcurl4-gnutls-dev=7.68.0-1ubuntu2.21 \
+    libperl-dev=5.30.0-9ubuntu0.5 \
     && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

docker/scripts/install_htslib.sh

@@ -5,7 +5,7 @@ set -euo pipefail
 apt-get update && apt-get install --no-install-recommends \
     libbz2-dev=1.0.8-2 \
     liblzma-dev=5.2.4-1ubuntu1.1 \
-    libssl-dev=1.1.1f-1ubuntu2.19 \
+    libssl-dev=1.1.1f-1ubuntu2.20 \
     -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

docker/scripts/install_ldak.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+set -euo pipefail
+
+wget --no-check-certificate https://dougspeed.com/wp-content/uploads/ldak5.2.linux_.zip
+unzip ldak5.2.linux_.zip
+cp ldak5.2.linux /bin/ldak

docker/scripts/install_metal.sh

@@ -2,9 +2,11 @@
 set -euo pipefail
 
 # metal
-wget --no-check-certificate http://csg.sph.umich.edu/abecasis/metal/download/Linux-metal.tar.gz && \
-   tar -xvzf Linux-metal.tar.gz && \
-   rm -rf  Linux-metal.tar.gz
+wget --no-check-certificate https://github.com/statgen/METAL/archive/refs/tags/2020-05-05.tar.gz
+tar -xvzf 2020-05-05.tar.gz
 
-mv generic-metal/* .
-cp metal  /bin
+mkdir build && cd build
+cmake -DCMAKE_BUILD_TYPE=Release ../METAL-2020-05-05/.
+make -j4
+make install
+cp bin/metal /bin

docker/scripts/install_minimac4.sh

@@ -4,7 +4,7 @@ set -euo pipefail
 # install some deps for installing cget
 apt-get update && \
     apt-get install --no-install-recommends \
-    python3-pip=20.0.2-5ubuntu1.9 \
+    python3-pip=20.0.2-5ubuntu1.10 \
     python3-click=7.0-3 \
     python3-six=1.14.0-2 \
     -y && \

docker/scripts/install_qctools.sh

@@ -1,13 +1,29 @@
 #!/bin/sh
 set -euo pipefail
 
-# qctools
- wget --no-check-certificate https://www.well.ox.ac.uk/~gav/resources/qctool_v2.0.6-Ubuntu16.04-x86_64.tgz && \
-    tar -xvzf qctool_v2.0.6-Ubuntu16.04-x86_64.tgz && \
-    rm -rf  qctool_v2.0.6-Ubuntu16.04-x86_64.tgz
+# python appears to be a build time dependency
+apt-get update && apt-get install -y  --no-install-recommends python3=3.8.2-0ubuntu2 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# /usr/bin/python must exist
+update-alternatives --install /usr/bin/python python /usr/bin/python3 10
 
+# qctools
+wget --no-check-certificate https://code.enkre.net/qctool/zip/e5723df2c0c85959/qctool.zip
+unzip qctool.zip
+cd qctool
+./waf configure
+./waf
 
-mv qctool_v2.0.6-Ubuntu16.04-x86_64/* .
-cp qctool  /bin
+# copy binaries to /bin
+cp build/release/apps/inthinnerator_v2.2.2 /bin/inthinnerator
+cp build/release/apps/hptest_v2.2.2 /bin/hptest
+cp build/release/apps/ldbird_v2.2.2 /bin/ldbird
+cp build/release/apps/qctool_v2.2.2 /bin/qctool
+cp build/release/apps/selfmap_v2.2.2 /bin/selfmap
 
-chmod 755 /bin/qctool
+# remove python
+apt-get purge \
+    python3 -y && \
+    apt-get autoremove --purge -y

docker/scripts/install_snptest.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -euo pipefail
+
+# snptest
+wget --no-check-certificate http://www.well.ox.ac.uk/~gav/resources/snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz
+tar -xvzf snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz
+cp snptest_v2.5.6_CentOS_Linux7.8.2003-x86_64_dynamic/snptest_v2.5.6 /bin/snptest