gemBS index failure: bgzip not found

[paul-sud]

We are trying to upgrade our version of gemBS to 8b33580390dd0f975dbb0f7e3f72ed34ce7b17c1 (v 3.5.0), and are getting an error about bgzip not found when trying to make to create the gemBS index:

FileNotFoundError: [Errno 2] No such file or directory: 'bgzip': 'bgzip'

In the previous version of gemBS we were using (this commit: 7256070f8ed0b01dfd53601f40fa05d7497df542), we did not have this issue. If I compare the Docker containers, in the old version I can find the bgzip in the following folder:

root@9b7b16e0d597:/software# ls /root/.local/lib/python3.7/site-packages/gemBS/bin
bcftools  bgzip  htsfile  samtools  tabix

Whereas with the new gemBS I can't find it there, which could explain the error:

root@5f64f63fce99:/software# ls /root/.local/lib/python3.7/site-packages/gemBS/bin
bcftools  samtools

Is there some other directory that I need to add to PATH? Or some other installation I need to do in the Dockerfile? Apologies if I am missing something. You can see the Docker build output here if need be: https://circleci.com/gh/ENCODE-DCC/wgbs-pipeline/760.

I can see bgzip as well as the other two now missing binaries tabix and htsfile all being compiled successfully in there, so maybe it is just an issue of copying them over to the Python site-packages?

Thanks,

Paul

[heathsc]

Hi Paul,

Ah got it. I moved the htslib build directory but didn't update the installation script. I will update it on the site, but if you want you can just change line 114 of setup.py from:

    for htslib in glob.glob("tools/samtools/htslib*"):

to:

    for htslib in glob.glob("tools/htslib"):

Simon

On Fri, Mar 20, 2020 at 7:17 PM Paul Sud notifications@github.com wrote:

We are trying to upgrade our version of gemBS to 8b33580 https://github.com/heathsc/gemBS/commit/8b33580390dd0f975dbb0f7e3f72ed34ce7b17c1 (v 3.5.0), and are getting an error about bgzip not found when trying to make to create the gemBS index:

FileNotFoundError: [Errno 2] No such file or directory: 'bgzip': 'bgzip'

In the previous version of gemBS we were using (this commit: 7256070 https://github.com/heathsc/gemBS/commit/7256070f8ed0b01dfd53601f40fa05d7497df542), we did not have this issue. If I compare the Docker containers, in the old version I can find the bgzip in the following folder:

root@9b7b16e0d597:/software# ls /root/.local/lib/python3.7/site-packages/gemBS/bin bcftools bgzip htsfile samtools tabix

Whereas with the new gemBS I can't find it there, which could explain the error:

root@5f64f63fce99:/software# ls /root/.local/lib/python3.7/site-packages/gemBS/bin bcftools samtools

Is there some other directory that I need to add to PATH? Or some other installation I need to do in the Dockerfile? Apologies if I am missing something. You can see the Docker build output here if need be: https://circleci.com/gh/ENCODE-DCC/wgbs-pipeline/760.

I can see bgzip as well as the other two now missing binaries tabix and htsfile all being compiled successfully in there, so maybe it is just an issue of copying them over to the Python site-packages?

Thanks,

Paul

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[paul-sud]

Thanks Simon. I updated our Dockerfile to use the new commit you pushed and the index completes successfully now.

[heathsc]

Thanks for the report - I had had one other report of that bug but I hadn't tracked down the problem!

On Fri, Mar 20, 2020 at 8:25 PM Paul Sud notifications@github.com wrote:

Thanks Simon. I updated our Dockerfile to use the new commit you pushed and the index completes successfully now.

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