SetUp/cgat at master · moelzek/SetUp · GitHub

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-- 25 JAN 17 --
Following the instructions from the cgatwiki on how to install cgat code collection:
https://cgatwiki.anat.ox.ac.uk/xwiki/bin/view/CGAT/Conda
--> 'Install the development version of the CGAT code (from GitHub)'

# add cgat channel
> conda config --add channels cgat

> source activate cgat_test

> conda install cgat-devel

Run into following error:
(cgat_test) tss38@workstation-tom:~/git_repos$ lsb_release -a
bash: lsb_release: command not found

Looks like I need to install lsb_release:

Following instructions here:
https://www.unixmen.com/linux-troubleshooting-fix-lsb_release-command-found-centos/

> sudo yum provides */lsb_release

> sudo yum install redhat-lsb-core

> sudo yum install redhat-lsb

--> No error with repeat command:
> conda install cgat-devel

Install cgat code:
> python setup.py develop

Got error when running python:
> import GTF as GTF
ImportError: No module named 'bx'

No bx-python 3.5 available on conda. So...
> pip install bx-python

CGATPipelines:
> git clone git@github.com:CGATOxford/CGATPipelines.git

> python setup.py develop
Runs into error:
error: ggplot 0.6.8 is installed but ggplot>=0.9.3 is required by {'CGATReport'}

Resolve with:
> conda install ggplot=0.11.5

-- 26 JAN 17 --
Next error:
./rpy/rinterface/_rinterface.c:80:31: fatal error: readline/readline.h: No such file or directory
 #include <readline/readline.h>

Resolve with:
> yum install readline-devel

----------
Next error:
Error: pg_config executable not found.

Resolve with:
> sudo yum install postgresql-devel

----------
Next error:
alignlib_lite.cpp:288:32: fatal error: boost/shared_ptr.hpp: No such file or directory
 #include "boost/shared_ptr.hpp"

Resolve with :
> sudo yum install boost-devel

NO MORE ERRORS!!!


-- 27 JAN 17 - CGATREPORT --
cgatreport throws an error with the ggplot version specified in the
cgat-devel conda environment:

When running make build_report with readqc pipeline:
Exception occurred:
  File "/home/FILESERVER5/proteomics/tss38/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 859, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.VersionConflict: (ggplot 0.6.8 (/home/FILESERVER5/proteomics/tss38/anaconda3/lib/python3.5/site-packages), Requirement.parse('ggplot>=0.9.3'))

resolved with (conda-forge update):
> conda install ggplot=0.11.5