Skip to content

Commit b12c3b8

Browse files
espenhgnespenhgn
committed
bump plink version
1 parent 93c25ac commit b12c3b8

6 files changed

Lines changed: 18 additions & 17 deletions

File tree

‎docker/scripts/install_plink.sh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
set -euo pipefail
33

44
# plink
5-
wget --no-check-certificate https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20231211.zip && \
6-
unzip -j plink_linux_x86_64_20231211.zip && \
7-
rm -rf plink_linux_x86_64_20231211.zip
5+
wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v1.9.0-b.7.11/plink_linux_x86_64.zip && \
6+
unzip -j plink_linux_x86_64.zip && \
7+
rm -rf plink_linux_x86_64.zip
88
cp plink /bin

‎docs/containers/README.md‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ Here is a brief overview of available container [files](./../../containers/READM
44

55
* [hello.sif](hello.md) - a simple container for demo purpose, allowing to experiment with Apptainer/Singularity features
66
* [gwas.sif](gwas.md) - multiple tools (released as binaries/executables) for imputation and GWAS analysis
7-
* [python3.sif](python3.md) - python3 environment with pre-installed modules and tools
8-
* [r.sif](r.md) - R 4.0.5 environment with rareGWAMA, GenomicSEM, TwoSampleMR and GSMR packages installed (plus some standard R packages)
7+
* [python3.sif](python3.md) - python3 environment with pre-installed modules and tools (Jupyter, Scipy, Pandas, scikit-learn, etc.)
8+
* [r.sif](r.md) - R/RStudio environment with rareGWAMA, GenomicSEM, TwoSampleMR and GSMR packages installed (plus many standard R packages)
99

1010
All containers have a common set of linux tools like ``gzip``, ``tar``, ``parallel``, etc.
1111
Please open an issue if you'd like to add more of such basic tools.

‎docs/containers/gwas.md‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ List of software included in the container:
2828

2929
| OS/tool | version | license
3030
| ------------------------------- | ----------------------------------------- | -------------
31-
| ubuntu | 20.04 | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
31+
| ubuntu | 24.04LTS | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
3232
| bcftools[^bcftools] | 1.19 | [MIT/Expat/GPLv3](https://github.com/samtools/bcftools/blob/develop/LICENSE)
3333
| bedtools[^bedtools] | 2.31.1 | [MIT](https://opensource.org/licenses/MIT)
3434
| beagle[^beagle1] [^beagle2] | 22Jul22.46e | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
@@ -48,12 +48,12 @@ List of software included in the container:
4848
| liftOver[^liftover] | latest | [permissive](https://genome-store.ucsc.edu)
4949
| metal[^metal] | 2020-05-05 | -
5050
| minimac4[^minimac4] | v4.1.6 | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
51-
| plink[^plink19] | v1.90b7.2 64-bit (11 Dec 2023) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
52-
| plink2[^plink2] | v2.00a5.10LM 64-bit Intel (5 Jan 2024) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
53-
| plink2_avx2[^plink2] | v2.00a5.10LM AVX2 Intel (5 Jan 2024) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
51+
| plink[^plink19] | v1.9.0-b.7.11 64-bit (19 Aug 2025) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
52+
| plink2[^plink2] | v2.0.0-a.6.23LM 64-bit Intel (24 Aug 2025) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
53+
| plink2_avx2[^plink2] | v2.0.0-a.6.23LM AVX2 Intel (24 Aug 2025) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
5454
| PRSice_linux[^prsice] | 2.3.5 | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
55-
| qctool[^qctool] | 2.2.2, revision e5723df2c0c85959 | [Boost](https://www.boost.org/LICENSE_1_0.txt)
56-
| regenie[^regenie] | v3.6 | [MIT/Boost](https://github.com/rgcgithub/regenie/blob/master/LICENSE)
55+
| (qctool[^qctool]) | 2.2.2, revision e5723df2c0c85959 | [Boost](https://www.boost.org/LICENSE_1_0.txt)
56+
| regenie[^regenie] | v4.1.2 | [MIT/Boost](https://github.com/rgcgithub/regenie/blob/master/LICENSE)
5757
| samtools[^bcftools] | v1.19.2 | [MIT/ExpatD](https://github.com/samtools/samtools/blob/develop/LICENSE)
5858
| shapeit4.2[^shapeit4] | v4.2.2 | [MIT](https://opensource.org/licenses/MIT)
5959
| shapeit5[^shapeit5] phase_rare | v5.1.1 | [MIT](https://opensource.org/licenses/MIT)

‎docs/containers/hello.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -94,7 +94,7 @@ List of software included in the container:
9494
| OS/tool | version | license
9595
| ------------------- |------------------------------------------ | -------------
9696
| ubuntu | 20.04 | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
97-
| plink[^1] | v1.90b6.18 64-bit (16 Jun 2020) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
97+
| plink[^1] | v1.9.0-b.7.11 64-bit (19 Aug 2025) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
9898

9999
### References
100100

‎docs/containers/python3.md‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -33,9 +33,10 @@ List of software in the container:
3333

3434
| OS/tool | version | license
3535
| --------------------------- | ----------------------------------------- | -------------
36-
| ubuntu | 20.04 (LTS) | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
36+
| ubuntu | 24.04 (LTS) | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
3737
| LDpred[^ldpred] | 1.0.11 | [MIT](https://opensource.org/licenses/MIT)
38-
| plink[^plink19] | v1.90b6.18 64-bit (16 Jun 2020) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
38+
| plink[^plink19] | v1.9.0-b.7.11 64-bit (19 Aug 2025) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
39+
| Miniforge | 25.3.1-0 | [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause)
3940
| python3[^python3] | python 3.10.6 + numpy, pandas, etc. | [PSF](https://docs.python.org/3.10/license.html)
4041
| python_convert[^convert] | git SHA bcde562 | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
4142

‎docs/containers/r.md‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -59,10 +59,10 @@ List of main software in the container:
5959

6060
| OS/tool | version | license
6161
| ------------------------- | ----------------------------------------- | -------------
62-
| ubuntu | 22.04.5 | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
63-
| R[^r] | 4.4.1 (2024-09-04) + data.table, ggplot, etc. | [misc](https://www.r-project.org/Licenses/)
62+
| ubuntu | 24.04LTS | [Creative Commons CC-BY-SA version 3.0 UK licence](https://ubuntu.com/legal/intellectual-property-policy)
63+
| R[^r] | 4.5.1 (2025-06-13) + data.table, ggplot, etc. | [misc](https://www.r-project.org/Licenses/)
6464
| gcta64[^gcta] | 1.94.1 | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
65-
| GenomicSEM[^genomicsem] | [GenomicSEM/GenomicSEM@bcbbaff](https://github.com/GenomicSEM/GenomicSEM/commit/bcbbaffff5767acfc5c020409a4dc54fbf07876b) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
65+
| GenomicSEM[^genomicsem] | [GenomicSEM/GenomicSEM@8e0ef5](https://github.com/GenomicSEM/GenomicSEM/commit/8e0ef594e95885b1f734f1dfcfe668b16ada2880) | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
6666
| GSMR[^gsmr] | v1.0.9 | [GPL>=v2](https://www.gnu.org/licenses/gpl-2.0.html)
6767
| rareGWAMA[^raregwama] | [dajiangliu/rareGWAMA@72e962d](https://github.com/dajiangliu/rareGWAMA/commit/72e962dae19dc07251244f6c33275ada189c2126) | -
6868
| seqminer[^seqminer] | [zhanxw/seqminer@142204d](https://github.com/zhanxw/seqminer/commit/142204d1005553ea87e1740ff97f0286291e41f9) | [GPL](https://github.com/zhanxw/seqminer/blob/master/LICENSE)

0 commit comments

Comments
 (0)