Installation of PLINK2 on docker issues

[Vesalius Tx]

I have a simple docker:

FROM python:3.10-bookworm

# Install PLINK
RUN mkdir -p ~/plink && \
    cd ~/plink && pwd && ls -la && \
    wget -O ./plink2.zip https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip && \
     unzip -t -v ./plink2.zip && \
     unzip -v ./plink2.zip && \
     pwd && ls -la && \
     chmod a+x ./plink2

I've added chmod just to make sure that the plink2 has been unarchived, but it does not. Here is the output of this RUN:
#8 [ 3/24] RUN mkdir -p ~/plink &&     cd ~/plink && pwd && ls -la &&     wget -O ./plink2.zip https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip &&     unzip -t -v ./plink2.zip &&     unzip -v ./plink2.zip &&     pwd && ls -la &&     chmod a+x ./plink2
#8 0.202 /root/plink
#8 0.209 total 8
#8 0.209 drwxr-xr-x 2 root root 4096 Sep 10 21:59 .
#8 0.209 drwx------ 1 root root 4096 Sep 10 21:59 ..
#8 0.228 --2025-09-10 21:59:22--  https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip
#8 0.238 Resolving s3.amazonaws.com (s3.amazonaws.com)... 52.217.233.72, 54.231.137.160, 52.217.38.38, ...
#8 0.273 Connecting to s3.amazonaws.com (s3.amazonaws.com)|52.217.233.72|:443... connected.
#8 0.398 HTTP request sent, awaiting response... 200 OK
#8 0.576 Length: 7518206 (7.2M) [application/zip]
#8 0.576 Saving to: ‘./plink2.zip’
#8 1.022 2025-09-10 21:59:23 (16.1 MB/s) - ‘./plink2.zip’ saved [7518206/7518206]
#8 1.022
#8 1.026 Archive:  ./plink2.zip
#8 1.026     testing: plink2                   OK
#8 1.165     testing: vcf_subset               OK
#8 1.181     testing: intel-simplified-software-license.txt   OK
#8 1.181 No errors detected in compressed data of ./plink2.zip.
#8 1.182 Archive:  ./plink2.zip
#8 1.182  Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
#8 1.182 --------  ------  ------- ---- ---------- ----- --------  ----
#8 1.182 24818328  Defl:N  6538598  74% 2025-09-02 04:29 c45f3f94  plink2
#8 1.182  2409784  Defl:N   977148  60% 2025-09-02 04:28 275375e1  vcf_subset
#8 1.182     4139  Defl:N     1948  53% 2025-09-02 04:30 47400563  intel-simplified-software-license.txt
#8 1.182 --------          -------  ---                            -------
#8 1.182 27232251          7517694  72%                            3 files
#8 1.183 /root/plink
#8 1.184 total 7352
#8 1.184 drwxr-xr-x 2 root root    4096 Sep 10 21:59 .
#8 1.184 drwx------ 1 root root    4096 Sep 10 21:59 ..
#8 1.184 -rw-r--r-- 1 root root 7518206 Sep  2 04:36 plink2.zip
#8 1.197 chmod: cannot access './plink2': No such file or directory
#8 ERROR: process "/bin/sh -c mkdir -p ~/plink &&     cd ~/plink && pwd && ls -la &&     wget -O ./plink2.zip https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip &&     unzip -t -v ./plink2.zip &&     unzip -v ./plink2.zip &&     pwd && ls -la &&     chmod a+x ./plink2" did not complete successfully: exit code: 1
------
 > [ 3/24] RUN mkdir -p ~/plink &&     cd ~/plink && pwd && ls -la &&     wget -O ./plink2.zip https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip &&     unzip -t -v ./plink2.zip &&     unzip -v ./plink2.zip &&     pwd && ls -la &&     chmod a+x ./plink2:
1.182  2409784  Defl:N   977148  60% 2025-09-02 04:28 275375e1  vcf_subset
1.182     4139  Defl:N     1948  53% 2025-09-02 04:30 47400563  intel-simplified-software-license.txt
1.182 --------          -------  ---                            -------
1.182 27232251          7517694  72%                            3 files
1.183 /root/plink
1.184 total 7352
1.184 drwxr-xr-x 2 root root    4096 Sep 10 21:59 .
1.184 drwx------ 1 root root    4096 Sep 10 21:59 ..
1.184 -rw-r--r-- 1 root root 7518206 Sep  2 04:36 plink2.zip
1.197 chmod: cannot access './plink2': No such file or directory

It looks like unzip does nothing. What am I doing wrong?!

Thanks in advance,
Nick

[Matthew Maher]

this isn't really a PLINK question.   But you seem to have called unzip twice, both times with '-v', which I believe means "show the info, but don't do actually anything".  You should just try the commands manually one by one.

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