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Latest Bowtie2 build doesn't include version #22836

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rpetit3 opened this issue Jun 23, 2020 · 2 comments
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Latest Bowtie2 build doesn't include version #22836

rpetit3 opened this issue Jun 23, 2020 · 2 comments

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@rpetit3
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rpetit3 commented Jun 23, 2020

The current build of Bowtie2 does not output version number.

bowtie2 --version
/home/rpetit/miniconda3/envs/bactopia-1.3.1/bin/bowtie2-align-s version
...truncated...

The expected output is:

bowtie2 --version
/home/rpetit/miniconda3/envs/bactopia-1.3.1/bin/bowtie2-align-s version 2.4.1
...truncated...

After digging it looks like this is related to the change in: #22545 (specifically 5dd7114).

Bowtie2 uses the VERSION file to specifiy the version (See: https://github.com/BenLangmead/bowtie2/blob/b4911f20a7a701df57dd1889d6eee0134d1ec895/Makefile#L328)

Related issue on Bowtie Repo: BenLangmead/bowtie2#301

I can see about submitting a PR to bowtie2 that would allow VERSION to be set at command line instead of only being available from the file.
@cblume
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cblume commented Jun 24, 2020

I was about to open this issue as well. A result of this bug is SAM headers missing the value to the VN: key, which renders the header--and in turn, the whole file--invalid.

@rpetit3 rpetit3 mentioned this issue Jun 30, 2020
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marcelm added a commit to elsasserlab/minute that referenced this issue Jun 30, 2020
@marcelm
Pin Bowtie2 to a working version
4c78fde 
Bowtie2 2.4.1, which we get otherwise at the moment, is packaged incorrectly
in Bioconda, see <bioconda/bioconda-recipes#22836>.
@marcelm marcelm mentioned this issue Jun 30, 2020
Merged
rpetit3 added a commit that referenced this issue Jul 2, 2020
@rpetit3
Update meta.yaml
55c45dc 
The pin for Bowtie2 is related to #22836
BiocondaBot added a commit that referenced this issue Jul 3, 2020
@BiocondaBot
[ci skip] Merge PR 22967
c1d90c1 
Merge PR #22967, commits were: 
 * Update build.sh

Bactopia changed how versions were handled
 * Update meta.yaml

The pin for Bowtie2 is related to #22836
 * Update bactopia to 1.4.0
This was referenced Aug 19, 2020
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Open
MikkelSchubert added a commit to MikkelSchubert/paleomix that referenced this issue Sep 26, 2020
@MikkelSchubert
exclude bowtie2.4.x from conda install
6458b92 
Due to a bug in the conda build script, these versions of bowtie2 have
no version information. This results bowtie2 inserting empty VN values
in @pg tags, resulting in invalid SAM headers.

bioconda/bioconda-recipes#22836
@bernt-matthias bernt-matthias mentioned this issue Nov 2, 2020
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@bernt-matthias
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Seems to be fixed in the latest version

@rpetit3 rpetit3 mentioned this issue Mar 4, 2021
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marcelm added a commit to elsasserlab/minute that referenced this issue Oct 28, 2021
@marcelm
Bump Bowtie to 2.4.4
e6e6996 
The reason for restricting the version to 2.3.5.1 was that the tool would
create incorrect VN tags in the SAM header, see #51. This bug has since
been fixed according to
bioconda/bioconda-recipes#22836 .

The upstream issue at BenLangmead/bowtie2#301 was
re-opened, though.

Closes #121
@marcelm marcelm mentioned this issue Oct 28, 2021
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@cblume @rpetit3 @bernt-matthias