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Update setup.md #8

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Update setup.md #8

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Commits on Jul 30, 2020

  1. Update setup.md 

    *Maybe first a stupid question: but do you need to state that for the analysis a UNIX operating system is necessary? I know that this is probably obvious, just wanted to make sure.
*Then I again made some minor text changes (please revise them and revert if you feel they made things worse).
*Specific issues:
   *Line 28-40: I could not install snakemake with the command you provided, probably because my python was too new? I got the following error:

`UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - snakemake==5.2 -> python[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']

Your python: python=3.7'

   *Line 57: I followed the other commands to install majiq, but installation of the last command failed for me. I will try to attach a log file, which might help you (and me) to understand why... at first glance it seems to have a problem with gcc, i.e. with my C compiler and C++ compiler.

   *Line 69: I could not install devtools with the given command. several packages were not available:
' ERROR: dependencies ‘usethis’, ‘covr’, ‘httr’, ‘rversions’ are not available for package ‘devtools’
* removing ‘/home/volker/miniconda3/envs/leafcutter/lib/R/library/devtools’
'

   *Line 87: first of all, you probably need to tell people where to find the "junctionseq.yml", although you point this out at the top, I would probably re-iterate here to make sure people understand. Then, I simply could not run the command:

'(base) volker@gehring-workstation1:~/Tools/baltica/envs$ conda env create -f junctionseq-env.yml --yes
usage: conda-env [-h] {create,export,list,remove,update,config} ...
conda-env: error: unrecognized arguments: --yes
'
Hope those comments help in any way. I would be happy to try to fix those problems. Maybe they are mostly because of issues with my machine...
    @boehmv
    boehmv authored Jul 30, 2020
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