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nanoporetech / pomoxis

Analysis components from Oxford Nanopore Research
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Error downloading porechop? #20

Closed ScarabMonkey closed 4 years ago

ScarabMonkey commented 6 years ago

When I try to make install I get an error that it can't find Porechop - I have actually already compiled porechop and it is available from this commandline using simply 'porechop' so I'm not sure why pomoxis installer doesn't find it. Pip knows it's already installed - but pomoxis seems to be trying to find it on pypi.org...

pip install git+https://github.com/rrwick/Porechop
Collecting git+https://github.com/rrwick/Porechop
  Cloning https://github.com/rrwick/Porechop to /tmp/pip-8a0i93tf-build
  Requirement already satisfied (use --upgrade to upgrade): porechop==0.2.3 from git+https://github.com/rrwick/Porechop in /net/zeta/usr/mbu/software/anaconda3/lib/python3.6/site-packages
Installed /net/zeta/usr/packages/nanoporetech/pomoxis/venv/lib/python3.6/site-packages/pomoxis-0.1.11-py3.6.egg
Processing dependencies for pomoxis==0.1.11
Searching for Porechop
Reading https://pypi.org/simple/Porechop/
Couldn't find index page for 'Porechop' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.org/simple/
No local packages or working download links found for Porechop
error: Could not find suitable distribution for Requirement.parse('Porechop')
make: *** [install] Error 1
cjw85 commented 6 years ago

Hi @ScarabMonkey

How are you trying to set up pomoxis?

The current Makefile builds a virtual environment and compiles/installs all third party binaries and packages into it. Along the way it should install porechop from its github repo, there's a stage where pip install -r requirements.txt is run within the environment.

Your error above appears to have arisen when python setup.py install has run without porechop being installed into the environment.

The installation does not depend on, and will ignore, any versions of porechop you have on your existing path.

ScarabMonkey commented 6 years ago

I'm following the install guide - just running 'make install'. The first time I ran this, I hadn't configured a proxy so it failed to download porechop - but after adding the proxy to my environment the make continued on and built loads of stuff (after I added some 'devel' packages)...

OS: CentOS 7.5 with OpenHPC modules for gnu7 Python: Anaconda3

cjw85 commented 6 years ago

We don't have much experience with CentOS (we almost exclusively work on Ubuntu, and a bit of macOS), I'll start by trying to reproduce your issue. As I noted above, I suspect its something to do with pip having trouble installing from a github repo.

ScarabMonkey commented 6 years ago

I actually have a feeling that the make is not re-running the requirements file after a half-successful previous attempt - is there a way I can force make to re-do the requirements?

cjw85 commented 6 years ago

The Makefile could definitely do with recovering failed builds better. Try the following (taken from the Makefile):

sh venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
python setup.py install
cjw85 commented 5 years ago

Hi @ScarabMonkey Is this working for you now?

avitalsteiman commented 5 years ago

Hi, I had this problem as well (although working with ubuntu) when i tried to run python setup.py install after pulling down a change ([(https://github.com/nanoporetech/pomoxis/issues/29] ). I tried running the commands you suggested above: sh venv/bin/activate pip install --upgrade pip pip install -r requirements and received the following error:

Could not find a version that satisfies the requirement Porechop (from -r pomoxis.egg-info/requires.txt (line 14)) (from versions: ) No matching distribution found for Porechop (from -r pomoxis.egg-info/requires.txt (line 14))

Any ideas? Thanks