Question: MACS2 files not found even just after successfully installing
0
gravatar for ariel.balter
2.8 years ago by
ariel.balter140
ariel.balter140 wrote:

Could someone please give me an idea of what might be going on here. I install macs2 using conda, which can find it, but it throws errors when I try to run it about not being able to find files.

balter@server:~$ conda install macs2
Fetching package metadata ...........
Solving package specifications: ..........

Package plan for installation in environment <server path>/users/balter/miniconda2:

The following NEW packages will be INSTALLED:

    macs2: 2.1.1.20160309-r3.2.2_0 bioconda

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###########################################################################################| 100%
balter@server:~$ which macs2
<server path>/users/balter/miniconda2/bin/macs2
balter@server:~$ macs2 -h
Traceback (most recent call last):
  File "<server path>/users/balter/miniconda2/bin/macs2", line 4, in <module>
    __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2')
  File "<server path>/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "<server path>/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 1496, in run_script
pkg_resources.ResolutionError: No script named 'macs2'
balter@server:~$ macs2 --version
Traceback (most recent call last):
  File "<server path>/users/balter/miniconda2/bin/macs2", line 4, in <module>
    __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2')
  File "<server path>/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "<server path>/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 1496, in run_script
pkg_resources.ResolutionError: No script named 'macs2'
macs2 software error • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Devon Ryan91k • written 2.8 years ago by ariel.balter140
1
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

I highly encourage you to use the bioconda channel, the quality of the packages will be better.

conda install -c bioconda macs2

Edit Make that conda install -c bioconda -c r macs2, since there's an R dependency that we fixed in that version. I've just tested this and it works (which is good, since I wrote the recipe for this one...) :)

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Devon Ryan91k

Thanks Devon. Unfortunately, I'm still getting the same error :(

balter@server:~$ conda install -c bioconda -c r macs2
Fetching package metadata ...........
Solving package specifications: ..........

Package plan for installation in environment <server path>/users/balter/miniconda2:

The following NEW packages will be INSTALLED:

    macs2: 2.1.1.20160309-r3.2.2_0 bioconda

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|############################################################################################################################################################################| 100%
balter@server:~$ which macs2
<server path>/users/balter/miniconda2/bin/macs2
balter@server:~$ macs2 --version
Traceback (most recent call last):
  File "<server path>/users/balter/miniconda2/bin/macs2", line 4, in <module>
    __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2')
  File "<server path>/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "<server path>/users/balter/miniconda2/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 1496, in run_script
pkg_resources.ResolutionError: No script named 'macs2'
ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by ariel.balter140

No clue, this isn't something that I can reproduce.

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

Phooey. Thanks for trying. I'll see if SO has any suggestions.

ADD REPLYlink written 2.8 years ago by ariel.balter140
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