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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
45 stars 6 forks source link

conda installation with OSX #122

Closed dputhier closed 4 years ago

dputhier commented 4 years ago

@guillaumecharbonnier Hi guillaume, When I'm trying to install pygtftk under OSX, I get:

╰─ conda install -c bioconda pygtftk
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

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

Output in format: Requested package -> Available versions

It seems that OSX and linux version are unsync on bioconda. Could you have a look please. Best

guillaumecharbonnier commented 4 years ago

Hi Denis,

I'll investigate why we currently have linux-64 v1.1.2 osx-64 v1.1.0

Nevertheless, you should still be able to get at least v1.1.0 instead of this rather uninformative conflict error.

Could you try to download this file https://raw.githubusercontent.com/guillaumecharbonnier/mw-lib/master/src/snakemake/envs/pygtftk.yaml Then run: conda env create -f pygtftk.yaml And let me know if you still have this error?

dputhier commented 4 years ago

It works.

guillaumecharbonnier commented 4 years ago

Hi @dputhier ,

Macos version is not built anymore because the BiocondaBot decided to skip osx: https://github.com/bioconda/bioconda-recipes/commit/05c33947f75c5932f8b5d7c964ecc6b011cc55e5#diff-c3793f153da86aba356737e0e4bac05b

Could you try on your Mac

git clone https://github.com/bioconda/bioconda-recipes
cd recipes/pygtftk/
# remove "osx" from the "skip" row in meta.yaml
conda-build .

If you see no build error I'll just try to commit the fix on bioconda.

dputhier commented 4 years ago

Hi @guillaumecharbonnier, I turned: skip: True # [py2k or osx] to skip: True # [py2k]

It failed... "conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {"bedtools[version='>=2.23']", "ftputil[version='>=3.3.1,<4.0.0']", "pybigwig[version='>=0.3']", "plotnine[version='>=0.4.0']", "pybedtools[version='>=0.7.8']"}"

All packages except plotnine version='>=0.4.0' are available. Would it be possible to ask installation of plotnine through pip ? Best

bedtools[version='>=2.23'] https://anaconda.org/bioconda/bedtools (2.29.2 OSX) ftputil[version='>=3.3.1,<4.0.0'] https://anaconda.org/conda-forge/ftputil pybigwig[version='>=0.3'] https://anaconda.org/bioconda/pybigwig pybedtools[version='>=0.7.8'] https://anaconda.org/bioconda/pybedtools https://anaconda.org/bioconda/pybedtools

Leaving build/test directories:
  Work:
 /Users/puthier/miniconda3/envs/python_dev_37/conda-bld/work
  Test:
 /Users/puthier/miniconda3/envs/python_dev_37/conda-bld/test_tmp
Leaving build/test environments:
  Test:
source activate

/Users/puthier/miniconda3/envs/python_dev_37/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol Build: source activate /Users/puthier/miniconda3/envs/python_dev_37/conda-bld/_build_env

Traceback (most recent call last):
  File

"/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda_build/environ.py", line 757, in get_install_actions actions = install_actions(prefix, index, specs, force=True) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated return f(*args, *kwds) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/plan.py", line 474, in install_actions txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction should_retry_solve) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff force_remove, should_retry_solve) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/core/solve.py", line 275, in solve_final_state ssc = self._add_specs(ssc) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/core/solve.py", line 555, in _add_specs explicit_pool = ssc.r._get_package_pool(self.specs_to_add) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/resolve.py", line 553, in _get_package_pool pool = self.get_reduced_index(specs) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated return f(args, **kwds) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/resolve.py", line 574, in get_reduced_index explicit_specs, features = self.verify_specs(explicit_specs) File "/Users/puthier/miniconda3/envs/python_dev_37/lib/python3.7/site-packages/conda/resolve.py", line 288, in verify_specs raise ResolvePackageNotFound(bad_deps) conda.exceptions.ResolvePackageNotFound:

Le mar. 2 juin 2020 à 10:20, guillaumecharbonnier notifications@github.com a écrit :

Hi @dputhier https://github.com/dputhier ,

Macos version is not built anymore because the BiocondaBot decided to skip osx: bioconda/bioconda-recipes@05c3394#diff-c3793f153da86aba356737e0e4bac05b https://github.com/bioconda/bioconda-recipes/commit/05c33947f75c5932f8b5d7c964ecc6b011cc55e5#diff-c3793f153da86aba356737e0e4bac05b

Could you try on your Mac

git clone https://github.com/bioconda/bioconda-recipes cd recipes/pygtftk/

remove "osx" from the "skip" row in meta.yaml

conda-build .

If you see no build error I'll just try to commit the fix on bioconda.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dputhier/pygtftk/issues/122#issuecomment-637374616, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAN7CHRBGOOEG2SLPEA5CBLRUSY3FANCNFSM4NKG73UQ .

--

Denis Puthier laboratoire INSERM TAGC/INSERM U 1090 Parc Scientifique de Luminy case 928 163, avenue de Luminy 13288 MARSEILLE cedex 09 FRANCE Mail: denis.puthier@univ-amu.fr Tel: (National) 04 91 82 87 31 / (International) 33 4 91 82 87 31 Fax: (National) 04 91 82 87 01 / (International) 33 4 91 82 87 01

Web:

http://tagc.univ-mrs.fr/tagc/index.php/research/network-bioinformatics/dputhier

====================================================================

guillaumecharbonnier commented 4 years ago

Could you check if you have these channels in the same order in your ~/.condarc ? Else, add them and retry the conda-build. I know channels can be added using this but I am unsure copy pasting the .condarc is equivalent.

show_channel_urls: true
channels:
  - conda-forge
  - bioconda
  - defaults
auto_update_conda: false
dputhier commented 4 years ago

I had no ~/.condarc so I added one with the indicated content and it worked. I have uploaded the package using the guillaumecharbonnier account. Best

Le mar. 2 juin 2020 à 23:15, guillaumecharbonnier notifications@github.com a écrit :

Could you check if you have these channels in the same order in your ~/.condarc ? Else, add them and retry the conda-build. I know channels can be added using this https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html but I am unsure copy pasting the .condarc is equivalent.

show_channel_urls: true channels:

  • conda-forge
  • bioconda
  • defaults auto_update_conda: false

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dputhier/pygtftk/issues/122#issuecomment-637810470, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAN7CHX6BG27M5VZEORCOQLRUVTVLANCNFSM4NKG73UQ .

--

Denis Puthier laboratoire INSERM TAGC/INSERM U 1090 Parc Scientifique de Luminy case 928 163, avenue de Luminy 13288 MARSEILLE cedex 09 FRANCE Mail: denis.puthier@univ-amu.fr Tel: (National) 04 91 82 87 31 / (International) 33 4 91 82 87 31 Fax: (National) 04 91 82 87 01 / (International) 33 4 91 82 87 01

Web:

http://tagc.univ-mrs.fr/tagc/index.php/research/network-bioinformatics/dputhier

====================================================================

guillaumecharbonnier commented 4 years ago

Perfect, bioconda will also have the latest version soon.