Fixed failed installation of minimac4 in gwas.sif (#196)

* `gwas.sif`: `test_gwas_minimac4` is failing Fixes #195 * rebuilt container * Adding misc packages for imputation (w.i.p.) * fixes * updated changelog etc. * added duohmm tool * added test * rebuild gwas.sif * flake8 complaints
comorment · Oct 17, 2023 · 00f7b51 · 00f7b51
1 parent 7e15724
commit 00f7b51
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -39,6 +39,30 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
+
+## [1.4.0] - 2023-10-18
+
+### Added
+
+* Added phasing/imputation tools ``beagle``, ``duohmm``, ``eagle``,  ``shapeit5``, ``switchError``, to ``gwas.sif`` container + updated tests
+
+### Fixed 
+
+* Fix issue that shell script wouldn't capture failing statements
+
+### Updated
+
+* Updated `gwas.sif` Dockerfile and installed shell scripts (misc. dependencies updates, installing ``gcta`` version 1.93.3beta2)
+* Rebuilt `gwas.sif` using Docker `--no-cache` option to fix missing `minimac4` binary, w. md5 checksum:
+
+  ```
+  a1dd235221902741bf5773945a584e47  singularity/gwas.sif
+  ```
+
+### Removed
+
+* Removed unused `install_miniconda.sh` script from `src/scripts` folder
+
 ## [1.3.9] - 2023-10-17
 
 ### Added
@@ -131,7 +155,7 @@ If MD5 sum is not listed for a certain release then it means that the container
 * Updated file and folder layout, fixing minor documentation issues. Moving from ``m2r2`` to ``Myst-parser`` for Sphinx-generated online docs.
 * Rebuilt the R container
 
-* ````
+* ```
   1d435af6003bbca95ef8cc062bf666fc  singularity/r.sif
   ```
 

diff --git a/docker/README.md b/docker/README.md
@@ -37,41 +37,50 @@ The detailed description of the available container [files](https://github.com/c
   | hello.sif         | ubuntu              | 20.04                                     | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
   | hello.sif         | plink               | v1.90b6.18 64-bit (16 Jun 2020)           | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | ubuntu              | 20.04                                     | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
-  | 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)
-  | 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          | simu_linux          | v0.9.4                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | gwas.sif          | bcftools            | 1.12 (using htslib 1.12)                  | [MIT/Expat/GPLv3](https://github.com/samtools/bcftools/blob/develop/LICENSE)
+  | gwas.sif          | beagle              | 22Jul22.46e                               | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | gwas.sif          | bgenix              | 1.1.7                                     | [Boost](https://www.boost.org/LICENSE_1_0.txt)
   | gwas.sif          | bolt                | v2.4 July 22, 2022                        | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-  | gwas.sif          | gcta64              | version 1.93.2 beta Linux                 | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | gwas.sif          | cat-bgen            | same version as bgenix                    | [Boost](https://www.boost.org/LICENSE_1_0.txt)
+  | gwas.sif          | duohmm              | 95bd395                                   | [MIT](https://opensource.org/licenses/MIT)
+  | gwas.sif          | eagle               | v2.4.1                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | gwas.sif          | edit-bgen           | same version as bgenix                    | [Boost](https://www.boost.org/LICENSE_1_0.txt)
+  | 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          | 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          | vcftools            | 0.1.17                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-  | gwas.sif          | bcftools            | 1.12 (using htslib 1.12)                  | [MIT/Expat/GPLv3](https://github.com/samtools/bcftools/blob/develop/LICENSE)
-  | gwas.sif          | flashpca_x86-64     | 2.0                                       | [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          | GWAMA               | 2.2.2                                     | [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause)
   | gwas.sif          | minimac4            | v4.1.0                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-  | gwas.sif          | bgenix              | 1.1.7                                     | [Boost](https://www.boost.org/LICENSE_1_0.txt)
-  | gwas.sif          | cat-bgen            | same version as bgenix                    | [Boost](https://www.boost.org/LICENSE_1_0.txt)
-  | gwas.sif          | edit-bgen           | same version as bgenix                    | [Boost](https://www.boost.org/LICENSE_1_0.txt)
-  | gwas.sif          | HTSlib              | 1.12                                      | [MIT/Expat/Modified-BSD](https://github.com/samtools/htslib/blob/develop/LICENSE)
+  | 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)
+  | 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          | 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)
+  | gwas.sif          | shapeit5 ligate     | v5.1.1                                    | [MIT](https://opensource.org/licenses/MIT)
+  | 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          | 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)
-  | python3.sif       | python3             | python 3.10.6 + numpy, pandas, etc.       | [PSF](https://docs.python.org/3.10/license.html)
   | python3.sif       | LDpred              | 1.0.11                                    | [MIT](https://opensource.org/licenses/MIT)
-  | python3.sif       | python_convert      | github commit bcde562                     | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | python3.sif       | plink               | v1.90b6.18 64-bit (16 Jun 2020)           | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
+  | python3.sif       | python3             | python 3.10.6 + numpy, pandas, etc.       | [PSF](https://docs.python.org/3.10/license.html)
+  | python3.sif       | python_convert      | github commit bcde562                     | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | r.sif             | ubuntu              | 20.04                                     | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
   | r.sif             | R                   | 4.0.5 (2021-03-31) + data.table, ggplot, etc. | [misc](https://www.r-project.org/Licenses/)
   | r.sif             | gcta64              | version 1.93.2 beta Linux                 | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-  | r.sif             | seqminer            | [zhanxw/seqminer@142204d](https://github.com/zhanxw/seqminer/commit/142204d1005553ea87e1740ff97f0286291e41f9)  | [GPL](https://github.com/zhanxw/seqminer/blob/master/LICENSE)
-  | r.sif             | rareGWAMA           | [dajiangliu/rareGWAMA@72e962d](https://github.com/dajiangliu/rareGWAMA/commit/72e962dae19dc07251244f6c33275ada189c2126)  | -
   | r.sif             | GenomicSEM          | [GenomicSEM/GenomicSEM@bcbbaff](https://github.com/GenomicSEM/GenomicSEM/commit/bcbbaffff5767acfc5c020409a4dc54fbf07876b)  | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-  | r.sif             | TwoSampleMR         | [MRCIEU/TwoSampleMR@c174107](https://github.com/MRCIEU/TwoSampleMR/commit/c174107cfd9ba47cf2f780849a263f37ac472a0e)  | [unknown/MIT](https://github.com/MRCIEU/TwoSampleMR#:~:text=Unknown%2C%20MIT%20licenses-,found,-Citation)
   | r.sif             | GSMR                | v1.0.9                                    | [GPL>=v2](https://www.gnu.org/licenses/gpl-2.0.html)
+  | r.sif             | rareGWAMA           | [dajiangliu/rareGWAMA@72e962d](https://github.com/dajiangliu/rareGWAMA/commit/72e962dae19dc07251244f6c33275ada189c2126)  | -
+  | r.sif             | seqminer            | [zhanxw/seqminer@142204d](https://github.com/zhanxw/seqminer/commit/142204d1005553ea87e1740ff97f0286291e41f9)  | [GPL](https://github.com/zhanxw/seqminer/blob/master/LICENSE)
+  | r.sif             | TwoSampleMR         | [MRCIEU/TwoSampleMR@c174107](https://github.com/MRCIEU/TwoSampleMR/commit/c174107cfd9ba47cf2f780849a263f37ac472a0e)  | [unknown/MIT](https://github.com/MRCIEU/TwoSampleMR#:~:text=Unknown%2C%20MIT%20licenses-,found,-Citation)
   | r.sif             | snpStats            | v1.40.0                                   | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | saige.sif         | ubuntu              | 16.04                                     | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
   | saige.sif         | SAIGE               | version 0.43                              | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)

diff --git a/docker/dockerfiles/gwas/Dockerfile b/docker/dockerfiles/gwas/Dockerfile
@@ -1,5 +1,5 @@
 # gwas container
-FROM 'ubuntu:20.04'
+FROM ubuntu:20.04
 
 ENV TZ=Europe
 ENV DEBIAN_FRONTEND noninteractive
@@ -83,7 +83,7 @@ COPY /scripts/install_vcftools.sh /tmp/vcftools/
 RUN bash /tmp/vcftools/install_vcftools.sh && \
     rm -rf /tmp/vcftools
 
-# HTSlib (dependency for bcftools & shapeit4)
+# HTSlib (dependency for bcftools & shapeit4++)
 WORKDIR /tmp/htslib
 COPY /scripts/install_htslib.sh /tmp/htslib/
 RUN bash /tmp/htslib/install_htslib.sh && \
@@ -134,4 +134,40 @@ COPY /scripts/patches/shapeit4.makefile.diff /tmp/shapeit4/
 RUN bash /tmp/shapeit4/install_shapeit4.sh && \
     rm -rf /tmp/shapeit4
 
+# shapeit5
+WORKDIR /tmp/shapeit5
+COPY /scripts/install_shapeit5.sh /tmp/shapeit5/
+COPY /scripts/patches/shapeit5.diff /tmp/shapeit5/
+COPY /scripts/patches/xcftools.diff /tmp/shapeit5/
+RUN bash /tmp/shapeit5/install_shapeit5.sh && \
+    rm -rf /tmp/shapeit5
+
+# eagle
+WORKDIR /tmp/eagle
+COPY /scripts/patches/eagle.diff /tmp/eagle/
+COPY /scripts/install_eagle.sh /tmp/eagle/
+RUN bash /tmp/eagle/install_eagle.sh && \
+    rm -rf /tmp/eagle
+
+# switchError
+WORKDIR /tmp/switchError
+COPY /scripts/patches/switchError.diff /tmp/switchError//
+COPY /scripts/install_switchError.sh /tmp/switchError/
+RUN bash /tmp/switchError/install_switchError.sh && \
+    rm -rf /tmp/switchError
+
+# beagle
+WORKDIR /tmp/beagle
+COPY /scripts/install_beagle.sh /tmp/beagle/
+COPY /scripts/stub.sh /tmp/beagle/
+RUN bash /tmp/beagle/install_beagle.sh && \
+    rm -rf /tmp/beagle
+
+
+# duohmm
+WORKDIR /tmp/duohmm
+COPY /scripts/install_duohmm.sh /tmp/duohmm/
+RUN bash /tmp/duohmm/install_duohmm.sh && \
+    rm -rf /tmp/duohmm
+
 WORKDIR /tools
diff --git a/docker/scripts/apt_get_essential.sh b/docker/scripts/apt_get_essential.sh
@@ -1,6 +1,8 @@
 #!/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 ca-certificates=20211016~20.04.1 && \
+apt-get update && apt-get install -y --no-install-recommends ca-certificates=20230311ubuntu0.20.04.1 && \
    update-ca-certificates
 
 # (!) Keep the list below sorted (!)
@@ -10,27 +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=7.68.0-1ubuntu2.14 \
+   curl=7.68.0-1ubuntu2.19 \
    dos2unix=7.4.0-2 \
    gfortran=4:9.3.0-1ubuntu2 \
-   git=1:2.25.1-1ubuntu3.6 \
+   git=1:2.25.1-1ubuntu3.11 \
    less=551-1ubuntu0.1 \
    libatlas-base-dev=3.10.3-8ubuntu7 \
-   libcurl4-openssl-dev=7.68.0-1ubuntu2.14 \
-   libgomp1=10.3.0-1ubuntu1~20.04 \
+   libcurl4-openssl-dev=7.68.0-1ubuntu2.19 \
+   libgomp1=10.5.0-1ubuntu1~20.04 \
    libgsl-dev=2.5+dfsg-6build1 \
-   libnss3=2:3.49.1-1ubuntu1.8 \
+   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=5.30.0-9ubuntu0.3 \
+   perl=5.30.0-9ubuntu0.4 \
    pkg-config=0.29.1-0ubuntu4 \
    tar=1.30+dfsg-7ubuntu0.20.04.2 \
    tofrodos=1.7.13+ds-4 \
    unzip=6.0-25ubuntu1.1 \
-   vim=2:8.1.2269-1ubuntu5.9 \
+   vim=2:8.1.2269-1ubuntu5.17 \
    wget=1.20.3-1ubuntu2 \
    zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5 \
    && \

diff --git a/docker/scripts/convert_docker_image_to_singularity.sh b/docker/scripts/convert_docker_image_to_singularity.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
+set -euo pipefail
 
-set -e
 # This script documents how to build the singularity container
 # from the Dockerfile
 

diff --git a/docker/scripts/install_bcftools.sh b/docker/scripts/install_bcftools.sh
@@ -1,11 +1,10 @@
 #!/bin/sh
-
-set -e
+set -euo pipefail
 
 # deps 
 apt-get update && apt-get install -y --no-install-recommends \
-    libcurl4-gnutls-dev=7.68.0-1ubuntu2.14 \
-    libperl-dev=5.30.0-9ubuntu0.3 \
+    libcurl4-gnutls-dev=7.68.0-1ubuntu2.19 \
+    libperl-dev=5.30.0-9ubuntu0.4 \
     && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

diff --git a/docker/scripts/install_beagle.sh b/docker/scripts/install_beagle.sh
@@ -0,0 +1,14 @@
+#!/bin/sh
+set -euo pipefail
+
+# additional deps
+apt-get update && apt-get install --no-install-recommends \
+    default-jre=2:1.11-72 \
+    -y && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+wget http://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar && \
+    mv beagle.22Jul22.46e.jar beagle.jar
+
+cat stub.sh beagle.jar > /usr/bin/beagle && chmod +x /usr/bin/beagle
diff --git a/docker/scripts/install_bgenix.sh b/docker/scripts/install_bgenix.sh
@@ -1,3 +1,6 @@
+#!/bin/sh
+set -euo pipefail
+
 # 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 && \

diff --git a/docker/scripts/install_bolt.sh b/docker/scripts/install_bolt.sh
@@ -1,4 +1,5 @@
 #!/bin/sh
+set -euo pipefail
 
 export VERSION="v2.3.5"
 

diff --git a/docker/scripts/install_duohmm.sh b/docker/scripts/install_duohmm.sh
@@ -0,0 +1,10 @@
+#!/bin/sh
+set -euo pipefail
+
+git clone https://github.com/jaredo/duohmm.git && \
+    cd duohmm && \
+    git checkout 95bd3958792aeaa43e9f301ead139e5691d7c165 && \
+    make -j 4 && \
+    cp bin/duohmm /usr/bin/
+
+
diff --git a/docker/scripts/install_eagle.sh b/docker/scripts/install_eagle.sh
@@ -0,0 +1,17 @@
+#!/bin/sh
+set -euo pipefail
+
+apt-get update && apt-get install --no-install-recommends \
+    libopenblas-dev=0.3.8+ds-1ubuntu0.20.04.1 \
+    -y && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+git clone --depth 1 -b v2.4.1 https://github.com/poruloh/Eagle.git && \
+    cd Eagle && \
+    git apply ../eagle.diff && \
+    cd src && \
+    make -j 4 && \
+    cp eagle /usr/bin/
+
+
diff --git a/docker/scripts/install_flashpca.sh b/docker/scripts/install_flashpca.sh
@@ -1,3 +1,6 @@
+#!/bin/sh
+set -euo pipefail
+
 wget --no-check-certificate https://github.com/gabraham/flashpca/releases/download/v2.0/flashpca_x86-64.gz && \
     gunzip flashpca_x86-64.gz && \
     chmod +x flashpca_x86-64 && \

diff --git a/docker/scripts/install_gcta.sh b/docker/scripts/install_gcta.sh
@@ -1,8 +1,9 @@
 #!/bin/sh
+set -euo pipefail
 
 # gcta
-curl -O -J -L https://yanglab.westlake.edu.cn/software/gcta/bin/gcta_1.93.2beta.zip && \
-    unzip -j  gcta_1.93.2beta.zip && \
-    rm -rf gcta_1.93.2beta.zip
+curl -O -J -L https://github.com/jianyangqt/gcta/releases/download/v1.93.3beta2/gcta_1.93.3beta2.zip && \
+    unzip -j  gcta_1.93.3beta2.zip && \
+    rm -rf gcta_1.93.3beta2.zip
 
 cp gcta64  /bin
diff --git a/docker/scripts/install_gctb.sh b/docker/scripts/install_gctb.sh
@@ -1,13 +1,11 @@
 #!/bin/sh
-
+set -euo pipefail
 
 # gctb
-
 wget --no-check-certificate https://cnsgenomics.com/software/gctb/download/gctb_2.02_Linux.zip  && \
    unzip   gctb_2.02_Linux.zip && \
    rm -rf gctb_2.02_Linux.zip
 
-
 mv gctb_2.02_Linux/* .
 cp gctb /bin 
 

diff --git a/docker/scripts/install_gwama.sh b/docker/scripts/install_gwama.sh
@@ -1,3 +1,6 @@
+#!/bin/sh
+set -euo pipefail
+
 wget --no-check-certificate http://www.geenivaramu.ee/tools/GWAMA_v2.2.2.zip && \
     unzip GWAMA_v2.2.2.zip && \
     make && \

diff --git a/docker/scripts/install_htslib.sh b/docker/scripts/install_htslib.sh
@@ -1,12 +1,11 @@
 #!/bin/sh
-
-set -e
+set -euo pipefail
 
 # additional deps
 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-1ubuntu2.16 \
+    libssl-dev=1.1.1f-1ubuntu2.19 \
     -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

diff --git a/docker/scripts/install_king.sh b/docker/scripts/install_king.sh
@@ -1,4 +1,5 @@
 #!/bin/sh
+set -euo pipefail
 
 # deps
 apt-get update && apt-get install --no-install-recommends \

diff --git a/docker/scripts/install_mambaforge.sh b/docker/scripts/install_mambaforge.sh
@@ -1,3 +1,6 @@
+#!/bin/sh
+set -euo pipefail
+
 curl -sSL https://github.com/conda-forge/miniforge/releases/download/4.14.0-0/Mambaforge-4.14.0-0-$(uname)-$(uname -m).sh -o /tmp/mambaforge.sh \
   && mkdir /root/.conda \
   && bash /tmp/mambaforge.sh -bfp /usr/local \

diff --git a/docker/scripts/install_metal.sh b/docker/scripts/install_metal.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
-
+set -euo pipefail
 
 # metal
 wget --no-check-certificate http://csg.sph.umich.edu/abecasis/metal/download/Linux-metal.tar.gz && \

diff --git a/docker/scripts/install_miniconda.sh b/docker/scripts/install_miniconda.sh
diff --git a/docker/scripts/install_minimac4.sh b/docker/scripts/install_minimac4.sh
@@ -1,9 +1,10 @@
 #!/bin/sh
+set -euo pipefail
 
 # install some deps for installing cget
 apt-get update && \
     apt-get install --no-install-recommends \
-    python3-pip=20.0.2-5ubuntu1.6 \
+    python3-pip=20.0.2-5ubuntu1.9 \
     python3-click=7.0-3 \
     python3-six=1.14.0-2 \
     -y && \

diff --git a/docker/scripts/install_plink.sh b/docker/scripts/install_plink.sh
@@ -1,4 +1,6 @@
 #!/bin/sh
+set -euo pipefail
+
 # plink
 wget --no-check-certificate https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20200616.zip && \
     unzip -j plink_linux_x86_64_20200616.zip && \