gwas.sif: Include samtools, bedtools, liftOver; upgrade others

Fixes #219
comorment · Feb 2, 2024 · da6e4e2 · da6e4e2
2 parents 432db66 + 842638d
commit da6e4e2
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Showing 9 changed files with 135 additions and 46 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -39,7 +39,7 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
-## [1.6.0] - 2024-02-02
+## [1.7.0] - 2024-02-02
 
 ### Added
 
@@ -71,7 +71,20 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Broken `docker/scripts/build_docker.sh` script
 
-## [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
 

diff --git a/docker/README.md b/docker/README.md
@@ -49,12 +49,13 @@ 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              | 1.94.1                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | gctb                | 2.04.3                                    | [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              | 1.19.1                                    | [MIT/Expat/Modified-BSD](https://github.com/samtools/htslib/blob/develop/LICENSE)
   | gwas.sif          | king                | 2.3.2                                     | [permissive](https://www.kingrelatedness.com/Download.shtml)
   | gwas.sif          | liftOver            | latest                                    | [permissive](https://genome-store.ucsc.edu)
-  | 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            | v4.1.6                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | plink               | v1.90b7.2 64-bit (11 Dec 2023)            | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | plink2              | v2.00a5.10LM 64-bit Intel (5 Jan 2024)    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
@@ -69,6 +70,7 @@ 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 (git SHA: d511f469e)               | [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)

diff --git a/docker/dockerfiles/gwas/Dockerfile b/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/

diff --git a/docker/scripts/apt_get_essential.sh b/docker/scripts/apt_get_essential.sh
@@ -14,6 +14,7 @@ apt-get update && apt-get install -y --no-install-recommends \
    cmake=3.16.3-1ubuntu1.20.04.1 \
    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 \

diff --git a/docker/scripts/install_ldak.sh b/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
diff --git a/docker/scripts/install_metal.sh b/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
diff --git a/docker/scripts/install_qctools.sh b/docker/scripts/install_qctools.sh
@@ -16,7 +16,11 @@ fossil checkout e5723df2c0c85959  # 2.2.2
 
 ./waf configure --prefix=/usr/
 ./waf install
-ln -s /usr/bin/qctool_v2.2.2 /usr/bin/qctool
+mv /usr/bin/hptest_v2.2.2 /usr/bin/hptest
+mv /usr/bin/inthinnerator_v2.2.2 /usr/bin/inthinnerator
+mv /usr/bin/ldbird_v2.2.2 /usr/bin/ldbird
+mv /usr/bin/qctool_v2.2.2 /usr/bin/qctool
+mv /usr/bin/selfmap_v2.2.2 /usr/bin/selfmap
 
 # remove fossil used to build qctools
 apt-get purge \

diff --git a/docker/scripts/install_snptest.sh b/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