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Published 20 hours ago • verified publisher icon arpcard

[BUG] lxml doesn't install from bioconda rgi-5.2.0

Open biobrad opened this issue 3 years ago • 3 comments

Hey guys, just a heads up, when installing from bioconda rgi-5.2.0 doesn't install the lxml dependency. An error is encountered when using auto_load for databases.

I installed lxml and then then it worked fine.

here is the method that i used when I installed the environment:

$ conda create -n rgi-card -c bioconda rgi=5.2.0 Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done

Package Plan

environment location: /home/harbj019/miniconda3/envs/rgi-card

added / updated specs: - rgi=5.2.0

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
_libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
_openmp_mutex-4.5          |            1_gnu          22 KB  conda-forge
bamtools-2.5.1             |       h9a82719_9        1012 KB  bioconda
beautifulsoup4-4.9.3       |     pyhb0f4dca_0          86 KB  conda-forge
biopython-1.72             |py36h14c3975_1000         2.4 MB  conda-forge
blast-2.9.0                |  pl526he19e7b1_7        19.5 MB  bioconda
cryptography-35.0.0        |   py36hb60f036_0         1.5 MB  conda-forge
diamond-0.8.36             |       h2e03b76_5         508 KB  bioconda
filetype-1.0.7             |     pyh9f0ad1d_0          13 KB  conda-forge
kma-1.3.25                 |       h5bf99c6_0         229 KB  bioconda
libblas-3.9.0              |12_linux64_openblas          12 KB  conda-forge
libcblas-3.9.0             |12_linux64_openblas          12 KB  conda-forge
libgfortran-ng-11.2.0      |      h69a702a_11          19 KB  conda-forge
liblapack-3.9.0            |12_linux64_openblas          12 KB  conda-forge
libtiff-4.2.0              |       hf544144_3         590 KB  conda-forge
oligoarrayaux-3.8          |       hc9558a2_0         165 KB  bioconda
patsy-0.5.2                |     pyhd8ed1ab_0         188 KB  conda-forge
pyahocorasick-1.4.0        |   py36h8c4c3a4_2          35 KB  conda-forge
pyfaidx-0.6.3.1            |     pyh5e36f6f_0          29 KB  bioconda
pyparsing-3.0.6            |     pyhd8ed1ab_0          79 KB  conda-forge
python_abi-3.6             |          2_cp36m           4 KB  conda-forge
seaborn-0.11.2             |       hd8ed1ab_0           4 KB  conda-forge
soupsieve-2.3              |     pyhd8ed1ab_0          33 KB  conda-forge
statsmodels-0.12.2         |   py36he33b4a0_0        11.4 MB  conda-forge
tbb-2021.4.0               |       h4bd325d_1         2.0 MB  conda-forge
------------------------------------------------------------
                                       Total:        39.9 MB

here is the error:

(rgi-card) harbj019@ssventer ~ $ rgi auto_load Traceback (most recent call last): File "/home/harbj019/miniconda3/envs/rgi-card/bin/rgi", line 4, in MainBase() File "/home/harbj019/miniconda3/envs/rgi-card/lib/python3.6/site-packages/app/MainBase.py", line 82, in init getattr(self, args.command)() File "/home/harbj019/miniconda3/envs/rgi-card/lib/python3.6/site-packages/app/MainBase.py", line 164, in auto_load self.auto_load_run(args) File "/home/harbj019/miniconda3/envs/rgi-card/lib/python3.6/site-packages/app/MainBase.py", line 171, in auto_load_run app.auto_load.main(args) File "/home/harbj019/miniconda3/envs/rgi-card/lib/python3.6/site-packages/app/auto_load.py", line 19, in main card_cannonical_version, card_variants_version = get_versions() File "/home/harbj019/miniconda3/envs/rgi-card/lib/python3.6/site-packages/app/auto_load.py", line 105, in get_versions soup = bs(r.content, 'lxml') File "/home/harbj019/miniconda3/envs/rgi-card/lib/python3.6/site-packages/bs4/init.py", line 246, in init % ",".join(features)) bs4.FeatureNotFound: Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?

the fix:

(rgi-card) harbj019@ssventer ~ $ conda install lxml Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/harbj019/miniconda3/envs/rgi-card

added / updated specs: - lxml

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
icu-69.1                   |       h9c3ff4c_0        13.2 MB  conda-forge
libxml2-2.9.12             |       h885dcf4_1         760 KB  conda-forge
libxslt-1.1.33             |       h0ef7038_3         521 KB  conda-forge
lxml-3.8.0                 |           py36_0         3.8 MB  conda-forge
------------------------------------------------------------
                                       Total:        18.3 MB

The following NEW packages will be INSTALLED:

icu conda-forge/linux-64::icu-69.1-h9c3ff4c_0 libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0 libxml2 conda-forge/linux-64::libxml2-2.9.12-h885dcf4_1 libxslt conda-forge/linux-64::libxslt-1.1.33-h0ef7038_3 lxml conda-forge/linux-64::lxml-3.8.0-py36_0

Proceed ([y]/n)? y

Downloading and Extracting Packages lxml-3.8.0 | 3.8 MB | ########################################################################################################################################## | 100% icu-69.1 | 13.2 MB | ########################################################################################################################################## | 100% libxslt-1.1.33 | 521 KB | ########################################################################################################################################## | 100% libxml2-2.9.12 | 760 KB | ########################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done

re-running auto_load:

rgi auto_load Directory '/home/harbj019/rgi_autoload_1weogk15' created =================================== DOWNLOAD CARD CANONICAL DATA =================================== --2021-11-29 06:36:05-- https://card.mcmaster.ca/download/0/broadstreet-v3.1.4.tar.bz2 Resolving card.mcmaster.ca (card.mcmaster.ca)... 130.113.77.126 Connecting to card.mcmaster.ca (card.mcmaster.ca)|130.113.77.126|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 3577605 (3.4M) [application/x-bzip2] Saving to: '/home/harbj019/rgi_autoload_1weogk15/data'

/home/harbj019/rgi_autoload_1weogk15/data 100%[==============================================================================================>] 3.41M 1.68MB/s in 2.0s

2021-11-29 06:36:08 (1.68 MB/s) - '/home/harbj019/rgi_autoload_1weogk15/data' saved [3577605/3577605]

=================================== DOWNLOAD CARD VARIANTS DATA =================================== --2021-11-29 06:36:09-- https://card.mcmaster.ca/download/6/prevalence-v3.0.9.tar.bz2 Resolving card.mcmaster.ca (card.mcmaster.ca)... 130.113.77.126 Connecting to card.mcmaster.ca (card.mcmaster.ca)|130.113.77.126|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1107447022 (1.0G) [application/x-bzip2] Saving to: '/home/harbj019/rgi_autoload_1weogk15/variants'

/home/harbj019/rgi_autoload_1weogk15/variants 100%[==============================================================================================>] 1.03G 7.61MB/s in 3m 16s

2021-11-29 06:39:27 (5.38 MB/s) - '/home/harbj019/rgi_autoload_1weogk15/variants' saved [1107447022/1107447022]

=================================== CARD CANONICAL ANNOTATIONS =================================== =================================== CARD VARIANTS ANNOTATIONS =================================== Done writing wildcard_database_v3.0.9.fasta =================================== CLEAN OLD DATABASES =================================== =================================== LOAD DATABASES =================================== =================================== CHECK LOADED DATABASES =================================== card_canonical: 3.1.4 | card_variants: 3.0.9 | kmer_sizes: 61 =================================== DONE ===================================

biobrad avatar Nov 28 '21 20:11 biobrad

If you guys can silver a 5.2.1 release then I will update the bioconda recipe.

innovate-invent avatar Dec 03 '21 19:12 innovate-invent

@biobrad version 5.2.1 is released. Do you want to switch?

raphenya avatar Jan 21 '22 14:01 raphenya

Yeah sure. I will try out the new version. Thank you very much for the work you and your team do. Researchers would be in a lot of trouble if we didn't have people like yourselves.

On Sat, 22 Jan 2022, 12:58 am amos, @.***> wrote:

@biobrad https://github.com/biobrad version 5.2.1 is released. Do you want to switch?

— Reply to this email directly, view it on GitHub https://github.com/arpcard/rgi/issues/174#issuecomment-1018551607, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANITBGVBF44O3N43M6OIGSTUXFUQLANCNFSM5I5VTQNA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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biobrad avatar Jan 21 '22 18:01 biobrad