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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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conda install failed #119

Closed keyfm closed 5 years ago

keyfm commented 5 years ago

Hi,

I am trying to install srst2 via pip install --install-option="--prefix=${HOME}/bin" srst2/ but it fails.

The pip install finished with Successfully installed srst2, however, I get an error when executing ${HOME}/bin/srst2:

Traceback (most recent call last): File "./srst2", line 5, in <module> from pkg_resources import load_entry_point File "/cm/shared/c3ddb/python/3.5.2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2927, in <module> @_call_aside File "/cm/shared/c3ddb/python/3.5.2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2913, in _call_aside f(*args, **kwargs) File "/cm/shared/c3ddb/python/3.5.2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2940, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/cm/shared/c3ddb/python/3.5.2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 635, in _build_master ws.require(__requires__) File "/cm/shared/c3ddb/python/3.5.2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 943, in require needed = self.resolve(parse_requirements(requirements)) File "/cm/shared/c3ddb/python/3.5.2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 829, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'srst2==0.2.0' distribution was not found and is required by the application

Alternatively I tried installing via conda install srst2, which tells me I need to get an older python version:

`UnsatisfiableError: The following specifications were found to be in conflict:

Any advice how to get srst2 running is highly appreciated.

katholt commented 5 years ago

SRST2 uses Python 2.7, not compatible with Python 3 (it's on the wishlist to convert, but we don't have the person-power) https://github.com/katholt/srst2#installation

keyfm commented 5 years ago

thx for the clarification Kat.

I ended up creating a designated srst2 conda environment with py2.7. In case anybody is interested how that was done I paste the code below.

conda create --name srst2 # set up environment called srst2 conda activate srst2 # avtivate conda install -c bioconda srst2 # install rest2 and dependencies in environment conda install -c bioconda/label/cf201901 srst2 # -“-

best f

On 1 Mar 2019, at 15:22, Kat Holt notifications@github.com wrote:

SRST2 uses Python 2.7, not compatible with Python 3 (it's on the wishlist to convert, but we don't have the person-power) https://github.com/katholt/srst2#installation https://github.com/katholt/srst2#installation — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/katholt/srst2/issues/119#issuecomment-468799199, or mute the thread https://github.com/notifications/unsubscribe-auth/AfhwUhmyv_oICy7M9Vkfnfi6SmDTwsaEks5vSYvrgaJpZM4bZfRP.

smitha97 commented 3 years ago

Thank you for this code patch so much! I couldn't figure out how to bypass the python 3 that was installed on my computer and throwing up errors every time I tried to run the program.