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Re: Packaging gwamar for Debian

Hi Andreas, 
I have resolved all the issues listed in your mail. Still, if possible I would prefer to have a week more time to clean up console messages to be more clear and less confusing.

Please find my answers to your comments one by one:

 0. fixed, I attach version number to each zip file when building (the current version is 1.15.1)

  1. I have attached Apache License 2 in LICENSE file.

  2. Indeed I've searched "print " and found some results which  resolved. I've tested it on Python3.

  3. indeed, this was ugly, I've moved all external tools configuration to a separate config_tools.txt, and change accordingly to your proposal

  4. I've improved the information on what happens when no parameters are provided to the program. The error you were getting was caused because the default action "-a" parameter to set to a method which assumed some preprocessing. Now, I require the parameter to be explicitly set in console.

Best regards,

2015-11-21 18:53 GMT+01:00 Andreas Tille <andreas@an3as.eu>:

I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in Biology and Medicine
for official Debian.

I came across GWAMAR[1] and started the packaging in Debian Git[2].
When doing so I stumbled upons some issues in the download archive[3]:

  0. Just a comment:  It would be more convenient to find versioned
     download archives rather than versioned directories.  The
     rationale behind this is that you have files with the same name
     but different content.

  1. I did not found any explicite license statement neither at the
     website nor inside the code.  Could you be so kind to clarify

  2. At Bitbucket[4] you write:
       This software is written in Python, thus Python 2 or 3 is
       required to run GWAMAR.
     When trying to build with Python3 I've git some errors
     (basically in print statements with Python2 syntax.  Please
     let me know if you are interested in patches fixing this.

  3. I noticed that the default config file in the download archive
     contains several private PATH settings.  I patched these to
     the Debian locations in the packaging git[5].  It would be
     great if you could change the default config file to a more
     neutral setting.

  4. Finally I endet up by an error message

       File "a1_save_details_scores_all.py", line 161, in <module>
         input_fh = open(input_fn)
       IOError: [Errno 2] No such file or directory: 'datasets/mtu173/exP//res_profiles.txt'

     I have no idea how to deal with this since this file is
     neither in the download tarball nor can I see it in the
     repository at Bitbucket.

I hope you like the intend to package GWAMAR for Debian and can
help with these issues.

Kind regards


[1] http://bioputer.mimuw.edu.pl/gwamar/
[2] git://anonscm.debian.org/debian-med/gwamar.git
[3] http://bioputer.mimuw.edu.pl/gwamar/software/gwamar_v1.14/gwamar.zip
[4] https://bitbucket.org/mimowo/gwamar
[5] https://anonscm.debian.org/cgit/debian-med/gwamar.git/tree/debian/patches/adapt_debian_locations_of_binaries.patch


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