Let's get this on Bioconda!

rpetit3 commented 2 years ago

Hi @mmcguffi, I'm creating this issue to work on getting this added to Bioconda. I think it would be straightforward.

One thing I was wondering about, would you be up for creating a plannotate download function to download the databases and put them in the expected location? I think this would make pLannotate easier to use for novice users, but also make the download process more standardized.

Curious on your thoughts about this

mmcguffi commented 2 years ago

Hi @rpetit3 thanks so much for opening this issue! I have considered that in the past, and I am definitely open to this option. Would a simple curl of the location of the GitHub-stored binaries (eg: https://github.com/barricklab/pLannotate/releases/download/v1.1.0/BLAST_dbs.tar.gz) suffice or do you have a better suggestion?

rpetit3 commented 2 years ago

Yep, I think keep it simple, so curl or wget is fine.

I think the big thing is plannotate download (or setupdb you get to come up with it), would keep up with the link to the database. This way if the link changes its not up to the user to track down the new link, your downloader would already have it.

For example (not saying you would change them, haha but it happens) https://github.com/barricklab/pLannotate/releases/download/v1.1.0/BLAST_dbs.tar.gz https://github.com/barricklab/pLannotate/releases/download/v1.1.1/blast_DBS.tar.gz https://github.com/barricklab/pLannotate/releases/download/v1.2.0/blast_dbs.tar.gz https://github.com/barricklab/pLannotate/releases/download/v2.0.0/BLAST_DBs.tar.gz

These changes would be handled by you, and be invisible to the user since they would just run the download command.

mmcguffi commented 2 years ago

Ok @rpetit3, I've implemented plannotate setupdb and it seems to be working smoothly! I hear what you're saying about the database versioning, so I have a dynamic solution (though it requires that the BLAST_dbs.tar.gz file to be consistently named).

Should I create a new release for these changes, or is there something else I should add for Bioconda first?

Thanks so much again!

rpetit3 commented 2 years ago

I think that should work, and if you get a new release with it we can start the bioconda process

mmcguffi commented 2 years ago

Great, I just published a new release with these changes: https://github.com/barricklab/pLannotate/releases/tag/v1.2.0

rpetit3 commented 2 years ago

Going to work on this later this week! Will update soon

rpetit3 commented 2 years ago

Started PR here https://github.com/bioconda/bioconda-recipes/pull/32760 Will keep you posted

rpetit3 commented 2 years ago

Hi @mmcguffi

pLannotate is now available on Bioconda (https://anaconda.org/bioconda/plannotate)! The main docs site (https://bioconda.github.io/) should capture it on the next build.

Please take some time to download it and test. Let me know if there are any issues and we can get it fixed.

Finally, anytime you create a new release the Bioconda Bot will create a new PR to update it.

Cheers! Robert

Going to close for now!

mmcguffi commented 2 years ago

Thanks so much @rpetit3! This is very generous of you and Im learning a lot looking at how you did this.

I am running into issues though -- I think the python version can be relaxed to python >= 3.7.0, since it did not work when trying to build into my 3.9.x environment and I can't see why there would be any conflicts with a higher python version. I think this change would be on the bioconda recipe side if I understand correctly?

That said, even when trying to build from a fresh conda environment, it failed with the below conflicts (my channels are set forge>bioconda>default; strict). Im not quite sure what the issue would be here since there are so many conflicts!

failed                                                                                                               -

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package tzdata conflicts for:
streamlit[version='>=1.2.0'] -> python[version='>=3.6'] -> tzdata
numpy -> python[version='>=3.10,<3.11.0a0'] -> tzdata
biopython[version='>1.77'] -> python[version='>=3.10,<3.11.0a0'] -> tzdata
bokeh[version='>=2.4.1'] -> python[version='>=3.10,<3.11.0a0'] -> tzdata
click -> python[version='>=3.9,<3.10.0a0'] -> tzdata
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> tzdata
pandas -> python[version='>=3.10,<3.11.0a0'] -> tzdata

Package xz conflicts for:
streamlit[version='>=1.2.0'] -> python[version='>=3.6'] -> xz[version='5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
click -> python[version='>=3.7,<3.8.0a0'] -> xz[version='5.0.*|5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
pandas -> python[version='>=3.10,<3.11.0a0'] -> xz[version='5.0.*|5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
biopython[version='>1.77'] -> python[version='>=3.7,<3.8.0a0'] -> xz[version='5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
diamond[version='>=2.0.13'] -> boost-cpp[version='>=1.74.0,<1.74.1.0a0'] -> xz[version='>=5.2.5,<5.3.0a0']
numpy -> python[version='>=3.8,<3.9.0a0'] -> xz[version='5.0.*|5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> xz[version='5.0.*|5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bokeh[version='>=2.4.1'] -> python[version='>=3.7,<3.8.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0']
python=3.7 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0']

Package six conflicts for:
numpy -> mkl-service[version='>=2.3.0,<3.0a0'] -> six
bokeh[version='>=2.4.1'] -> packaging[version='>=16.8'] -> six
streamlit[version='>=1.2.0'] -> altair[version='>=3.2.0'] -> six[version='>=1.4.0|>=1.5']
pandas -> python-dateutil[version='>=2.7.3'] -> six[version='>=1.5']

Package numpy conflicts for:
pandas -> bottleneck[version='>=1.2.1'] -> numpy[version='>=1.16.4,<2.0a0|>=1.21.3,<2.0a0']
streamlit[version='>=1.2.0'] -> numpy
numpy
streamlit[version='>=1.2.0'] -> altair[version='>=3.2.0'] -> numpy[version='1.11.*|1.12.*|1.13.*|>=0.18|>=1.21.5,<2.0a0|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.16.6,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.15.4,<2.0a0|>=1.14.6,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.12.1,<2.0a0|>=1.9.3,<2.0a0|>=1.11.*|>=1.9.*|>=1.21.2,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.11.3,<2.0a0|>=1.9.3,<1.10.0a0|>=1.16,<2.0a0|>=1.16,<1.20.0a0|>=1.14,<1.20.0a0|>=1.10,<1.20.0a0|>=1.10|>=1.11,<2.0a0|>=1.14,<2.0a0|>=1.15.3,<2.0a0|>=1.15.2,<2.0a0|>=1.21.3,<2.0a0|>=1.20.1,<2.0a0|>=1.20.0,<2.0a0|>=1.19.1,<2.0a0']
bokeh[version='>=2.4.1'] -> numpy[version='>=1.11.3']
pandas -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|>=1.11|>=1.11.*|>=1.12.1,<2.0a0|>=1.14.6,<2.0a0|>=1.15.4,<2.0a0|>=1.16.5,<2.0a0|>=1.16.6,<2.0a0|>=1.17.5,<2.0a0|>=1.18.5,<2.0a0|>=1.19.5,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.19.4,<2.0a0|>=1.19.2,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.9.3,<2.0a0|>=1.9.*|>=1.9|>=1.8|>=1.7|>=1.21.2,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.13.3,<2.0a0|>=1.11.3,<2.0a0|>=1.9.3,<1.10.0a0']
biopython[version='>1.77'] -> numpy

Package perl conflicts for:
blast[version='>=2.10.1'] -> entrez-direct -> perl[version='5.22.0.*|>=5.32.1,<6.0a0|>=5.26.0,<5.27.0a0|>=5.26.2,<5.27.0a0',build=*_perl5]
trnascan-se[version='>=2.0.7'] -> perl[version='>=5.26.2,<5.26.3.0a0|>=5.32.1,<5.33.0a0',build=*_perl5]
blast[version='>=2.10.1'] -> perl[version='>=5.26.2,<5.26.3.0a0']

Package tk conflicts for:
numpy -> python[version='>=3.8,<3.9.0a0'] -> tk[version='8.5.*|8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
pandas -> python[version='>=3.10,<3.11.0a0'] -> tk[version='8.5.*|8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
streamlit[version='>=1.2.0'] -> pillow[version='>=6.2.0'] -> tk[version='8.5.*|8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
click -> python[version='>=3.7,<3.8.0a0'] -> tk[version='8.5.*|8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> tk[version='8.5.*|8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
python=3.7 -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
bokeh[version='>=2.4.1'] -> pillow[version='>=7.1.0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.7,<8.7.0a0']
biopython[version='>1.77'] -> python[version='>=3.7,<3.8.0a0'] -> tk[version='8.5.*|8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
curl[version='>=7.81.0,<8.0a0'] -> krb5[version='>=1.19.2,<1.20.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0']

Package click conflicts for:
streamlit[version='>=1.2.0'] -> click[version='>=7.0|>=7.0,<8.0']
click

Package pyparsing conflicts for:
bokeh[version='>=2.4.1'] -> packaging[version='>=16.8'] -> pyparsing[version='<3,>=2.0.2|>=2.0.2,!=3.0.5|>=2.0.2,<3|>=2.0.2']
streamlit[version='>=1.2.0'] -> packaging -> pyparsing[version='<3,>=2.0.2|>=2.0.2,!=3.0.5|>=2.0.2,<3|>=2.0.2']

Package libedit conflicts for:
curl[version='>=7.81.0,<8.0a0'] -> krb5[version='>=1.19.2,<1.20.0a0'] -> libedit[version='>=3.1.20191231,<3.2.0a0|>=3.1.20191231,<4.0a0|>=3.1.20210216,<3.2.0a0|>=3.1.20210216,<4.0a0']
python=3.7 -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']

Package expat conflicts for:
numpy -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0']
python=3.7 -> pypy3.7=7.3.7 -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0']
click -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0']
bokeh[version='>=2.4.1'] -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.4.1,<3.0a0']
pandas -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0']
biopython[version='>1.77'] -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0']

Package curl conflicts for:
curl[version='>=7.81.0,<8.0a0']
blast[version='>=2.10.1'] -> curl[version='>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.77.0,<8.0a0|>=7.81.0,<8.0a0']

Package zlib conflicts for:
blast[version='>=2.10.1'] -> zlib[version='>=1.2.11,<1.3.0a0']
numpy -> python[version='>=3.8,<3.9.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
pandas -> python[version='>=3.10,<3.11.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
streamlit[version='>=1.2.0'] -> pillow[version='>=6.2.0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8']
click -> python[version='>=3.7,<3.8.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
diamond[version='>=2.0.13'] -> zlib[version='>=1.2.11,<1.3.0a0']
curl[version='>=7.81.0,<8.0a0'] -> libssh2[version='>=1.10.0,<2.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
python=3.7 -> zlib[version='>=1.2.11,<1.3.0a0']
bokeh[version='>=2.4.1'] -> pillow[version='>=7.1.0'] -> zlib[version='>=1.2.11,<1.3.0a0']
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
biopython[version='>1.77'] -> python[version='>=3.7,<3.8.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8']

Package typing_extensions conflicts for:
bokeh[version='>=2.4.1'] -> typing_extensions[version='>=3.10.0']
streamlit[version='>=1.2.0'] -> gitpython -> typing_extensions[version='>=3.7.4.3']
click -> importlib-metadata -> typing_extensions[version='>=3.6.4']

Package openssl conflicts for:
streamlit[version='>=1.2.0'] -> python[version='>=3.6'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
click -> python[version='>=3.7,<3.8.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1k,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
blast[version='>=2.10.1'] -> curl[version='>=7.81.0,<8.0a0'] -> openssl[version='>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0']
curl[version='>=7.81.0,<8.0a0'] -> krb5[version='>=1.19.2,<1.20.0a0'] -> openssl[version='>=1.1.1k,<1.1.2a']
python=3.7 -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1k,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a']
bokeh[version='>=2.4.1'] -> python[version='>=3.7,<3.8.0a0'] -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1k,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a']
biopython[version='>1.77'] -> python[version='>=3.7,<3.8.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1k,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
pandas -> python[version='>=3.10,<3.11.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
numpy -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']
curl[version='>=7.81.0,<8.0a0'] -> openssl[version='>=1.1.1l,<1.1.2a|>=3.0.0,<4.0a0']

Package pypy3.6 conflicts for:
numpy -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
numpy -> pypy3.6[version='>=7.3.1|>=7.3.2|>=7.3.3']

Package boost-cpp conflicts for:
streamlit[version='>=1.2.0'] -> pyarrow -> boost-cpp[version='>=1.68.0,<1.68.1.0a0|>=1.70.0,<1.70.1.0a0|>=1.72.0,<1.72.1.0a0|>=1.74.0,<1.74.1.0a0']
diamond[version='>=2.0.13'] -> boost-cpp[version='>=1.74.0,<1.74.1.0a0']

Package bzip2 conflicts for:
biopython[version='>1.77'] -> python[version='>=3.7,<3.8.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
python=3.7 -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
numpy -> python[version='>=3.8,<3.9.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
blast[version='>=2.10.1'] -> bzip2[version='>=1.0.8,<2.0a0']
streamlit[version='>=1.2.0'] -> python[version='>=3.6'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
diamond[version='>=2.0.13'] -> boost-cpp[version='>=1.74.0,<1.74.1.0a0'] -> bzip2[version='>=1.0.8,<2.0a0']
pandas -> python[version='>=3.10,<3.11.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
click -> python[version='>=3.7,<3.8.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
bokeh[version='>=2.4.1'] -> python[version='>=3.7,<3.8.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']

Package libcxxabi conflicts for:
python=3.7 -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='1|0|4|3|2|hcfea43d_1|hebd6815_0']
pandas -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='1|0|4|3|2|hcfea43d_1|hebd6815_0']
numpy -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='1|0|4|3|2|hcfea43d_1|hebd6815_0']

Package ca-certificates conflicts for:
click -> python -> ca-certificates
curl[version='>=7.81.0,<8.0a0'] -> openssl[version='>=3.0.0,<4.0a0'] -> ca-certificates
tabulate[version='>=0.8.9'] -> python[version='2.7.*|>=3.5'] -> ca-certificates
pandas -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python=3.7 -> openssl[version='>=3.0.0,<4.0a0'] -> ca-certificates
numpy -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates

Package pandas conflicts for:
streamlit[version='>=1.2.0'] -> altair[version='>=3.2.0'] -> pandas[version='>=0.18']
streamlit[version='>=1.2.0'] -> pandas[version='>=0.21.0|>=0.21.0,<1.3.0']
pandas

Package llvm-openmp conflicts for:
blast[version='>=2.10.1'] -> llvm-openmp[version='>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0']
numpy -> openblas[version='>=0.2.15'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=12.0.1|>=9.0.1|>=9.0.0']

Package packaging conflicts for:
streamlit[version='>=1.2.0'] -> packaging
bokeh[version='>=2.4.1'] -> packaging[version='>=16.8']
pandas -> numexpr[version='>=2.7.0'] -> packaging

Package setuptools conflicts for:
pandas -> setuptools[version='<60.0.0']
streamlit[version='>=1.2.0'] -> pandas[version='>=0.21.0'] -> setuptools[version='<60.0.0']
python=3.7 -> pip -> setuptools
bokeh[version='>=2.4.1'] -> jinja2[version='>=2.9'] -> setuptools
pandas -> numexpr[version='>=2.7.0'] -> setuptools

Package libcxx conflicts for:
blast[version='>=2.10.1'] -> libcxx[version='>=11.1.0|>=9.0.1']
blast[version='>=2.10.1'] -> pcre[version='>=8.45,<9.0a0'] -> libcxx[version='>=10.0.0|>=10.0.1']

Package libzlib conflicts for:
blast[version='>=2.10.1'] -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib==1.2.11[build='h9173be1_1012|h9173be1_1013']
blast[version='>=2.10.1'] -> libzlib[version='>=1.2.11,<1.3.0a0']
Note that strict channel priority may have removed packages required for satisfiability.

rpetit3 commented 2 years ago

For python, you'll want to relax the requirements here: https://github.com/barricklab/pLannotate/blob/master/setup.py#L60

As for the dependency issue, are you creating a new environment? And how does your base environment look?

Here's my base:

conda env export -n base
name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=4.5=1_gnu
  - brotlipy=0.7.0=py38h27cfd23_1003
  - bzip2=1.0.8=h7b6447c_0
  - c-ares=1.17.1=h27cfd23_0
  - ca-certificates=2021.7.5=h06a4308_1
  - certifi=2021.5.30=py38h06a4308_0
  - cffi=1.14.6=py38h400218f_0
  - chardet=4.0.0=py38h06a4308_1003
  - conda=4.10.3=py38h06a4308_0
  - conda-package-handling=1.7.3=py38h27cfd23_1
  - cryptography=3.4.7=py38hd23ed53_0
  - icu=58.2=he6710b0_3
  - idna=2.10=pyhd3eb1b0_0
  - kmc=3.1.2rc1=h2d02072_0
  - krb5=1.19.1=h3535a68_0
  - ld_impl_linux-64=2.35.1=h7274673_9
  - libarchive=3.5.1=hccf745f_2
  - libcurl=7.77.0=h2574ce0_0
  - libedit=3.1.20210216=h27cfd23_1
  - libev=4.33=h7b6447c_0
  - libffi=3.3=he6710b0_2
  - libgcc-ng=9.3.0=h5101ec6_17
  - libgomp=9.3.0=h5101ec6_17
  - libiconv=1.16=h516909a_0
  - libnghttp2=1.43.0=h812cca2_0
  - libsolv=0.7.18=h780b84a_0
  - libssh2=1.9.0=h1ba5d50_1
  - libstdcxx-ng=9.3.0=hd4cf53a_17
  - libxml2=2.9.12=h03d6c58_0
  - lz4-c=1.9.3=h2531618_0
  - lzo=2.10=h7b6447c_2
  - mamba=0.13.0=py38h2aa5da1_0
  - ncurses=6.2=he6710b0_1
  - openssl=1.1.1k=h27cfd23_0
  - pip=21.1.3=py38h06a4308_0
  - pycosat=0.6.3=py38h7b6447c_1
  - pycparser=2.20=py_2
  - pyopenssl=20.0.1=pyhd3eb1b0_1
  - pysocks=1.7.1=py38h06a4308_0
  - python=3.8.5=h7579374_1
  - python_abi=3.8=1_cp38
  - readline=8.1=h27cfd23_0
  - reproc=14.2.1=h36c2ea0_0
  - reproc-cpp=14.2.1=h58526e2_0
  - requests=2.25.1=pyhd3eb1b0_0
  - ruamel_yaml=0.15.100=py38h27cfd23_0
  - setuptools=52.0.0=py38h06a4308_0
  - six=1.16.0=pyhd3eb1b0_0
  - sqlite=3.36.0=hc218d9a_0
  - tk=8.6.10=hbc83047_0
  - tqdm=4.61.2=pyhd3eb1b0_1
  - urllib3=1.26.6=pyhd3eb1b0_1
  - wheel=0.36.2=pyhd3eb1b0_0
  - xz=5.2.5=h7b6447c_0
  - yaml=0.2.5=h7b6447c_0
  - zlib=1.2.11=h7b6447c_3
  - zstd=1.5.0=ha95c52a_0

Here's my conda create (used mamba because its so much quicker):

mamba create -n temp-plannotate -c conda-forge -c bioconda plannotate

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.13.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['plannotate']

pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) Done
bioconda/linux-64        [====================] (00m:00s) Done
conda-forge/noarch       [====================] (00m:01s) Done
conda-forge/linux-64     [====================] (00m:04s) Done
Transaction

  Prefix: /home/robert_petit/miniconda3/envs/temp-plannotate

  Updating specs:

   - plannotate

  Package                             Version  Build                 Channel                     Size
───────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────

  _libgcc_mutex                           0.1  conda_forge           conda-forge/linux-64      Cached
  _openmp_mutex                           4.5  1_gnu                 conda-forge/linux-64      Cached
  abseil-cpp                       20210324.2  h9c3ff4c_0            conda-forge/linux-64     1010 KB
  altair                                4.2.0  pyhd8ed1ab_1          conda-forge/noarch        711 KB
  argh                                 0.26.2  py37_1001             conda-forge/linux-64       33 KB
  argon2-cffi                          21.3.0  pyhd8ed1ab_0          conda-forge/noarch         15 KB
  argon2-cffi-bindings                 21.2.0  py37h5e8e339_1        conda-forge/linux-64       34 KB
  arrow-cpp                             6.0.1  py37he4d610e_8_cpu    conda-forge/linux-64       25 MB
  astor                                 0.8.1  pyh9f0ad1d_0          conda-forge/noarch         25 KB
  attrs                                21.4.0  pyhd8ed1ab_0          conda-forge/noarch        Cached
  aws-c-cal                            0.5.11  h95a6274_0            conda-forge/linux-64       37 KB
  aws-c-common                          0.6.2  h7f98852_0            conda-forge/linux-64      168 KB
  aws-c-event-stream                    0.2.7  h3541f99_13           conda-forge/linux-64       47 KB
  aws-c-io                             0.10.5  hfb6a706_0            conda-forge/linux-64      121 KB
  aws-checksums                        0.1.11  ha31a3da_7            conda-forge/linux-64       50 KB
  aws-sdk-cpp                         1.8.186  hb4091e7_3            conda-forge/linux-64        5 MB
  backcall                              0.2.0  pyh9f0ad1d_0          conda-forge/noarch         13 KB
  backports                               1.1  pyhd3eb1b0_0          pkgs/main/noarch            4 KB
  backports.functools_lru_cache         1.6.4  pyhd8ed1ab_0          conda-forge/noarch          9 KB
  backports.zoneinfo                    0.2.1  py37h5e8e339_4        conda-forge/linux-64       47 KB
  base58                                2.1.1  pyhd8ed1ab_0          conda-forge/noarch          9 KB
  biopython                              1.79  py37h5e8e339_1        conda-forge/linux-64        3 MB
  blast                                2.12.0  h3289130_1            bioconda/linux-64          22 MB
  bleach                                4.1.0  pyhd8ed1ab_0          conda-forge/noarch        121 KB
  blinker                                 1.4  py_1                  conda-forge/noarch         13 KB
  bokeh                                 2.4.2  py37h89c1867_0        conda-forge/linux-64       14 MB
  boost-cpp                            1.74.0  h359cf19_6            conda-forge/linux-64       16 MB
  boto3                               1.20.49  pyhd8ed1ab_0          conda-forge/noarch         71 KB
  botocore                            1.23.49  pyhd8ed1ab_0          conda-forge/noarch          5 MB
  brotlipy                              0.7.0  py37h5e8e339_1003     conda-forge/linux-64      342 KB
  bzip2                                 1.0.8  h7f98852_4            conda-forge/linux-64      Cached
  c-ares                               1.18.1  h7f98852_0            conda-forge/linux-64      Cached
  ca-certificates                  2021.10.26  h06a4308_2            pkgs/main/linux-64        Cached
  cachetools                            5.0.0  pyhd8ed1ab_0          conda-forge/noarch         12 KB
  certifi                           2021.10.8  py37h89c1867_1        conda-forge/linux-64      145 KB
  cffi                                 1.15.0  py37h036bc23_0        conda-forge/linux-64      225 KB
  charset-normalizer                   2.0.11  pyhd8ed1ab_0          conda-forge/noarch        Cached
  click                                 8.0.3  py37h89c1867_1        conda-forge/linux-64      145 KB
  cryptography                         36.0.1  py37hf1a17b8_0        conda-forge/linux-64        2 MB
  curl                                 7.81.0  h2574ce0_0            conda-forge/linux-64       90 KB
  debugpy                               1.5.1  py37hcd2ae1e_0        conda-forge/linux-64        2 MB
  decorator                             5.1.1  pyhd8ed1ab_0          conda-forge/noarch         12 KB
  defusedxml                            0.7.1  pyhd8ed1ab_0          conda-forge/noarch         23 KB
  diamond                              2.0.14  hdcc8f71_0            bioconda/linux-64           2 MB
  entrez-direct                          16.2  he881be0_0            bioconda/linux-64         Cached
  entrypoints                             0.4  pyhd8ed1ab_0          conda-forge/noarch          9 KB
  flit-core                             3.6.0  pyhd8ed1ab_0          conda-forge/noarch         42 KB
  freetype                             2.11.0  h70c0345_0            pkgs/main/linux-64        Cached
  fribidi                              1.0.10  h516909a_0            conda-forge/linux-64      113 KB
  gflags                                2.2.2  he1b5a44_1004         conda-forge/linux-64      114 KB
  giflib                                5.2.1  h516909a_2            conda-forge/linux-64       80 KB
  gitdb                                 4.0.9  pyhd8ed1ab_0          conda-forge/noarch         46 KB
  gitpython                            3.1.26  pyhd8ed1ab_0          conda-forge/noarch        123 KB
  glog                                  0.5.0  h48cff8f_0            conda-forge/linux-64      104 KB
  grpc-cpp                             1.42.0  ha1441d3_1            conda-forge/linux-64        4 MB
  icu                                    69.1  h9c3ff4c_0            conda-forge/linux-64      Cached
  idna                                    3.3  pyhd8ed1ab_0          conda-forge/noarch        Cached
  importlib-metadata                   4.10.1  py37h89c1867_0        conda-forge/linux-64       32 KB
  importlib_resources                   5.4.0  pyhd8ed1ab_0          conda-forge/noarch        Cached
  infernal                              1.1.4  h779adbc_0            bioconda/linux-64           3 MB
  ipykernel                             6.8.0  py37h6531663_0        conda-forge/linux-64      180 KB
  ipython                              7.31.1  py37h89c1867_0        conda-forge/linux-64        1 MB
  ipython_genutils                      0.2.0  py_1                  conda-forge/noarch         21 KB
  ipywidgets                            7.6.5  pyhd8ed1ab_0          conda-forge/noarch        101 KB
  jbig                                    2.1  h7f98852_2003         conda-forge/linux-64       43 KB
  jedi                                 0.18.1  py37h89c1867_0        conda-forge/linux-64      997 KB
  jinja2                                3.0.3  pyhd8ed1ab_0          conda-forge/noarch         99 KB
  jmespath                             0.10.0  pyh9f0ad1d_0          conda-forge/noarch         21 KB
  jpeg                                     9e  h7f98852_0            conda-forge/linux-64      269 KB
  jsonschema                            4.4.0  pyhd8ed1ab_0          conda-forge/noarch        Cached
  jupyter_client                        7.1.2  pyhd8ed1ab_0          conda-forge/noarch         90 KB
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  Summary:

  Install: 218 packages

  Total download: 513 MB

───────────────────────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n]

mmcguffi commented 2 years ago

@rpetit3 sorry this took me a bit to get back to you; I was trying to figure out what was going wrong, but I can't seem to nail down the provenance

In my problems above, I didn't add -c conda-forge along with the -c bioconda. After I did that though, I get the follow error using both mamba and conda to create an environment:

Preparing transaction: done
Verifying transaction: failed

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/._BLAST_dbs'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._Rfam.clanin'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._Rfam.cm'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._Rfam.cm.i1f'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._Rfam.cm.i1i'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._Rfam.cm.i1m'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._Rfam.cm.i1p'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._fpbase.dmnd'
specified in the package manifest cannot be found.

CondaVerificationError: The package for plannotate located at /Users/mmcguffi/opt/miniconda3/pkgs/plannotate-1.2.0-py37he5731a2_0
appears to be corrupted. The path 'lib/python3.7/site-packages/plannotate/data/BLAST_dbs/._swissprot.dmnd'
specified in the package manifest cannot be found.

(this is for mamba, but conda throws a similar error)

I think the issue here is somehow the path is appending a ._ in front of database location, but Im not sure where in the code this is coming from

rpetit3 commented 2 years ago

Hmmmm, this worked fine on Linux.

Maybe try a conda clean -ay

mcrone commented 2 years ago

How about a docker container for pLannotate? I've seen many bioconda packages seem to do this automatically?

mmcguffi commented 2 years ago

Hi @mcrone, I'm still having some issues with getting this working for mac via bioconda (seems to work fine for Linux) -- it has occurred to me that some people may finder docker easier/preferable, so I'll take a look into that as well

dpryan79 commented 2 years ago

Those . files do exist in the original conda package. These seem to be hold-overs from an OSX system, since the they contain quarantine information from OSX for downloaded files. Since the package that we distribute on bioconda was created under Linux, these were part of the original download. Since these have special meaning in OSX, it's highly likely that that's causing the issue. I will make a new package with loosened python restrictions that lacks these quarantine files.

dpryan79 commented 2 years ago

Small tip, when making the next database archive update, do it on the command line and run ls -a first so you can clean up the directory. There are a bunch of OSX files and archive attempts to set a bunch of OSX-specific quarantine warnings since apparently these are files you had downloaded.

mmcguffi commented 2 years ago

Thanks so much @dpryan79 !

However, I've looked through the database and I don't see these files. I even double checked that my system was showing me the all the files by running defaults write com.apple.finder AppleShowAllFiles YES before a simple ls -a

I see you added a line to the build.sh to remove these files, but I really can't find them when I download BLAST_dbs.tar.gz from the v1.1.0 releases page

I do see an accidental .DS_Store file though -- is this causing the issue?

dpryan79 commented 2 years ago

OSX is trying to be "helpful", those files are definitely there:

Anyway, the new build will be available in the next hour or so. Give that a whirl and , presuming it works, I can mark the old one as broken.

mmcguffi commented 2 years ago

Thanks @dpryan79 -- I actually had to spin up a Docker container in order to finally view those those ._ files...

I tried the new build on my mac (pyhdfd78af_1) and I still ran into the same issues -- my guess is that the rm BLAST_dbs/._* would be executed after after this error is thrown? At this point, I think maybe the easiest thing to do is to make a version bump and upload a clean db archive

mmcguffi commented 2 years ago

@dpryan79 I actually just uploaded a "clean" db archive to the existing release -- I think if line 14 in the meta.yaml is changed to https://github.com/barricklab/pLannotate/releases/download/v{{version}}/BLAST_dbs.tar.gz this should solve the OSX issues?

Im a bit unsure on this so your feedback would be much appreciated

dpryan79 commented 2 years ago

@mmcguffi The rm command is run before the package is built. When you install a conda package, it just downloads and extracts the tarball and nothing else, so it's impossible to run into that issue since those files aren't physically present in the package manifest. I expect conda just used the cached older build. If the blast db version is tied to the pLannotate version then yes, your proposed change should work.

mmcguffi commented 2 years ago

@dpryan79 I tried to fix this myself, but this is my first time directly contributing to Bioconda and the builds did not pass their checks.

My changes were pretty minuscule, so they only thing I can think of is that I messed up with the sha-256 checksum? I just ran shasum -a 256 BLAST_dbs.tar.gz on my command line and copy and pasted that -- Im not sure if that was the correct procedure...

mmcguffi commented 2 years ago

Finally got this sorted for OSX -- thanks so much for your help and time @rpetit3 and @dpryan79

mmcguffi / pLannotate

Let's get this on Bioconda! #12