Update shigatyper to 2.0.2 #37628

BiocondaBot · 2022-10-26T01:13:49Z

Update shigatyper: 2.0.1 → 2.0.2

Info	Link or Description
Recipe	`recipes/shigatyper` (click to view/edit other files)
Summary	Typing tool for Shigella spp. from WGS Illumina sequencing
Home	https://github.com/CFSAN-Biostatistics/shigatyper
Releases	https://github.com/CFSAN-Biostatistics/shigatyper/tags
Author	`@CFSAN-Biostatistics`

This pull request was automatically generated (see docs).

crashfrog · 2022-10-26T02:33:40Z

Build is failing on the basis of patch, but I don't understand the error:

2022-10-26T01:30:50.7264909Z 01:30:50 BIOCONDA INFO (OUT) ## Package Plan ##
2022-10-26T01:30:50.7265384Z 01:30:50 BIOCONDA INFO (OUT) 
2022-10-26T01:30:50.7266357Z 01:30:50 BIOCONDA INFO (OUT)   environment location: /opt/conda/conda-bld/shigatyper_1666747703048/_build_env
2022-10-26T01:30:50.7266999Z 01:30:50 BIOCONDA INFO (OUT) 
2022-10-26T01:30:50.7267283Z 01:30:50 BIOCONDA INFO (OUT) 
2022-10-26T01:30:50.7480686Z 01:30:50 BIOCONDA INFO (OUT) Source cache directory is: /opt/conda/conda-bld/src_cache
2022-10-26T01:30:50.7481564Z 01:30:50 BIOCONDA INFO (OUT) INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache
2022-10-26T01:30:50.7482310Z 01:30:50 BIOCONDA INFO (OUT) Downloading source to cache: conda-package-2.0.2_08df10fdcf.tar.gz
2022-10-26T01:30:50.7483118Z 01:30:50 BIOCONDA INFO (OUT) INFO:conda_build.source:Downloading source to cache: conda-package-2.0.2_08df10fdcf.tar.gz
2022-10-26T01:30:50.7483991Z 01:30:50 BIOCONDA INFO (OUT) Downloading https://github.com/CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.2.tar.gz
2022-10-26T01:30:50.7484899Z 01:30:50 BIOCONDA INFO (OUT) INFO:conda_build.source:Downloading https://github.com/CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.2.tar.gz
2022-10-26T01:30:50.7506697Z 01:30:50 BIOCONDA INFO (OUT) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): github.com:443
2022-10-26T01:30:50.9455609Z 01:30:50 BIOCONDA INFO (OUT) DEBUG:urllib3.connectionpool:https://github.com:443 "GET /CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.2.tar.gz HTTP/1.1" 302 0
2022-10-26T01:30:50.9480620Z 01:30:50 BIOCONDA INFO (OUT) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): codeload.github.com:443
2022-10-26T01:30:51.1582341Z 01:30:51 BIOCONDA INFO (OUT) DEBUG:urllib3.connectionpool:https://codeload.github.com:443 "GET /CFSAN-Biostatistics/shigatyper/tar.gz/refs/tags/conda-package-2.0.2 HTTP/1.1" 200 None
2022-10-26T01:30:51.1774655Z 01:30:51 BIOCONDA INFO (OUT) Success
2022-10-26T01:30:51.1775417Z 01:30:51 BIOCONDA INFO (OUT) INFO:conda_build.source:Success
2022-10-26T01:30:51.1775864Z 01:30:51 BIOCONDA INFO (OUT) Extracting download
2022-10-26T01:30:51.1926644Z 01:30:51 BIOCONDA INFO (OUT) Applying patch: /opt/recipe/add-index.patch
2022-10-26T01:30:51.3613819Z 01:30:51 BIOCONDA INFO (OUT) Applying patch: /opt/recipe/add-index.patch with args:
2022-10-26T01:30:51.3614591Z 01:30:51 BIOCONDA INFO (OUT) ['-Np1', '-i', '/tmp/tmp2pl7za3s/add-index.patch.native', '--binary']
2022-10-26T01:30:51.4153879Z 01:30:51 BIOCONDA INFO (OUT) checking file setup.py
2022-10-26T01:30:51.4154429Z 01:30:51 BIOCONDA INFO (OUT) Hunk #1 succeeded at 14 (offset 2 lines).
2022-10-26T01:30:51.4696316Z 01:30:51 BIOCONDA INFO (OUT) patching file setup.py
2022-10-26T01:30:51.4710867Z 01:30:51 BIOCONDA INFO (OUT) Hunk #1 succeeded at 14 (offset 2 lines).
2022-10-26T01:30:51.4712015Z 01:30:51 BIOCONDA INFO (OUT) Applying patch: /opt/recipe/add-outdir.patch
2022-10-26T01:30:51.6389218Z 01:30:51 BIOCONDA INFO (OUT) Applying patch: /opt/recipe/add-outdir.patch with args:
2022-10-26T01:30:51.6390262Z 01:30:51 BIOCONDA INFO (OUT) ['-Np1', '-i', '/tmp/tmpfgkobx86/add-outdir.patch.native', '--binary']
2022-10-26T01:30:51.6941234Z 01:30:51 BIOCONDA INFO (OUT) checking file shigatyper/shigatyper.py
2022-10-26T01:30:51.6953363Z 01:30:51 BIOCONDA INFO (OUT) Hunk #1 FAILED at 1.
2022-10-26T01:30:51.6953844Z 01:30:51 BIOCONDA INFO (OUT) Hunk #2 succeeded at 88 with fuzz 2 (offset 3 lines).
2022-10-26T01:30:51.6954279Z 01:30:51 BIOCONDA INFO (OUT) Hunk #3 succeeded at 509 (offset 3 lines).
2022-10-26T01:30:51.6954828Z 01:30:51 BIOCONDA INFO (OUT) Hunk #4 succeeded at 518 (offset 3 lines).
2022-10-26T01:30:51.6955322Z 01:30:51 BIOCONDA INFO (OUT) Hunk #5 succeeded at 559 with fuzz 2 (offset 3 lines).
2022-10-26T01:30:51.6955722Z 01:30:51 BIOCONDA INFO (OUT) Hunk #6 FAILED at 600.
2022-10-26T01:30:51.6956116Z 01:30:51 BIOCONDA INFO (OUT) 2 out of 6 hunks FAILED
2022-10-26T01:30:51.6985476Z 01:30:51 BIOCONDA INFO (OUT) Warning: failed to download source.  If building, will try again after downloading recipe dependencies.
2022-10-26T01:30:51.6986037Z 01:30:51 BIOCONDA INFO (OUT) Error was:
2022-10-26T01:30:51.6987311Z 01:30:51 BIOCONDA INFO (OUT) Command '['/opt/conda/bin/patch', '--no-backup-if-mismatch', '--batch', '-Np1', '-i', '/tmp/tmpfgkobx86/add-outdir.patch.native', '--binary', '--dry-run']' returned non-zero exit status 1.
2022-10-26T01:30:51.6988013Z 01:30:51 BIOCONDA INFO (OUT) Traceback (most recent call last):
2022-10-26T01:30:51.6988619Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
2022-10-26T01:30:51.6989072Z 01:30:51 BIOCONDA INFO (OUT)     sys.exit(main())
2022-10-26T01:30:51.6990001Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.7/site-packages/boa/cli/mambabuild.py", line 239, in main
2022-10-26T01:30:51.7001716Z 01:30:51 BIOCONDA INFO (OUT)     call_conda_build(action, config)
2022-10-26T01:30:51.7002607Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.7/site-packages/boa/cli/mambabuild.py", line 218, in call_conda_build
2022-10-26T01:30:51.7003135Z 01:30:51 BIOCONDA INFO (OUT)     **kwargs,
2022-10-26T01:30:51.7003810Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.7/site-packages/conda_build/api.py", line 195, in build
2022-10-26T01:30:51.7013732Z 01:30:51 BIOCONDA INFO (OUT)     variants=variants
2022-10-26T01:30:51.7014757Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.7/site-packages/conda_build/build.py", line 3093, in build_tree
2022-10-26T01:30:51.7027277Z 01:30:51 BIOCONDA INFO (OUT)     notest=notest,
2022-10-26T01:30:51.7030310Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.7/site-packages/conda_build/build.py", line 2138, in build
2022-10-26T01:30:51.7034962Z 01:30:51 BIOCONDA INFO (OUT)     try_download(m, no_download_source=False, raise_error=True)
2022-10-26T01:30:51.7036018Z 01:30:51 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.7/site-packages/conda_build/render.py", line 662, in try_download
2022-10-26T01:30:51.7043239Z 01:30:51 BIOCONDA INFO (OUT)     raise RuntimeError("Failed to download or patch source. Please see build log for info.")
2022-10-26T01:30:51.7045429Z 01:30:51 BIOCONDA INFO (OUT) RuntimeError: Failed to download or patch source. Please see build log for info.

@rpetit3 any idea?

rpetit3 · 2022-10-26T02:42:06Z

Would you be interested in me pushing these patches to the main repo? One was adding an option for --outdir and the other is including the index files.

Otherwise I can keep them here and just update the patch

crashfrog · 2022-10-26T02:49:50Z

Sure, I'm happy to accept a patch or PR to the shigatyper repo. Thanks!

rpetit3 · 2022-10-26T02:50:34Z

Want a submission now and rerelease or save it for v2.0.3?

rpetit3 · 2022-10-26T02:52:22Z

These patches stemmed from me improving docker container that's generated: #35161

crashfrog · 2022-10-26T02:52:39Z

I’d like to keep it on 2.0.2 if we can, just to avoid a skipped patch version. Does that work?

…

On Oct 26, 2022 at 9:50 AM +0700, Robert A. Petit III ***@***.***>, wrote: Want a submission now and rerelease or save it for v2.0.3? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

rpetit3 · 2022-10-26T02:55:02Z

No problem, I'll take it from here and get those PRs submitted your way

crashfrog · 2022-10-26T03:07:35Z

Awesome, thanks so much

…

On Wed, Oct 26, 2022 at 9:55 AM Robert A. Petit III < ***@***.***> wrote: No problem, I'll take it from here and get those PRs submitted your way — Reply to this email directly, view it on GitHub <#37628 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIFUSX3S4BTBDDXGHSGMALWFCMRBANCNFSM6AAAAAAROPZ5JA> . You are receiving this because you commented.Message ID: ***@***.***>

rpetit3 · 2022-10-26T03:43:53Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2022-10-26T03:44:27Z

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	shigatyper-2.0.2-pyhdfd78af_0.tar.bz2	LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with `docker`
shigatyper	2.0.2--pyhdfd78af_0	show `gzip -dc LinuxArtifacts/images/shigatyper:2.0.2--pyhdfd78af_0.tar.gz \| docker load`

rpetit3 · 2022-10-26T03:57:50Z

Conda

shigatyper --version
ShigaTyper 2.0.2

mkdir test_conda

shigatyper --SE ERR6005894SE.fastq.gz --name test_srr --outdir test_conda
... TRUNCATTED ...
sample  prediction      ipaB    notes
test_srr        Shigella dysenteriae Provisional serotype 96-265        +       this strain is ipaB+, suggesting that it retains the virulent invasion plasmid.

tree test_conda/
test_conda/
├── test_srr-hits.tsv
└── test_srr.tsv

cat test_conda/test_srr.tsv
sample  prediction      ipaB    notes
test_srr        Shigella dysenteriae Provisional serotype 96-265        +       this strain is ipaB+, suggesting that it retains the virulent invasion plasmid.

Docker

docker run --entrypoint /bin/bash --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/shigatyper:2.0.2--pyhdfd78af_0 -c "sh
igatyper --version" 2> /dev/null
ShigaTyper 2.0.2

docker run --entrypoint /bin/bash --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/shigatyper:2.0.2--pyhdfd78af_0 -c "sh
igatyper --SE /data/ERR6005894SE.fastq.gz --outdir /data/test_docker" 2> /dev/null
        Hit     Number of reads Length Covered  reference length        % covered       Number of variants      % accuracy
0       ipaH_c  32      740     780     94.9    0.0     100.0
1       ipaB    22      1015    1743    58.2    0.0     100.0
2       SdProv_wzx      16      1017    1320    77.0    0.0     100.0
3       SdProv_wzy      53      1104    1212    91.1    0.0     100.0
sample  prediction      ipaB    notes
ERR6005894SE    Shigella dysenteriae Provisional serotype 96-265        +       this strain is ipaB+, suggesting that it retains the virulent invasion plasmid

tree test_docker/
test_docker/
├── ERR6005894SE-hits.tsv
└── ERR6005894SE.tsv

cat test_docker/ERR6005894SE.tsv
sample  prediction      ipaB    notes
ERR6005894SE    Shigella dysenteriae Provisional serotype 96-265        +       this strain is ipaB+, suggesting that it retains the virulent invasion plasmid.

Everything looks good

rpetit3 · 2022-10-26T03:58:16Z

@BiocondaBot please merge

BiocondaBot · 2022-10-26T03:58:31Z

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

Update shigatyper to 2.0.2

bebfb7c

BiocondaBot added autobump Automatic Version Update new version labels Oct 26, 2022

Update add-outdir.patch

c3db766

rpetit3 approved these changes Oct 26, 2022

View reviewed changes

BiocondaBot merged commit 8b2c044 into master Oct 26, 2022

BiocondaBot deleted the bump/shigatyper branch October 26, 2022 03:59

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Update shigatyper to 2.0.2 #37628

Update shigatyper to 2.0.2 #37628

BiocondaBot commented Oct 26, 2022

crashfrog commented Oct 26, 2022 •

edited

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BiocondaBot commented Oct 26, 2022

Update shigatyper to 2.0.2 #37628

Update shigatyper to 2.0.2 #37628

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rpetit3 commented Oct 26, 2022

Conda

Docker

rpetit3 commented Oct 26, 2022

BiocondaBot commented Oct 26, 2022

crashfrog commented Oct 26, 2022 •

edited

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