Rostlab/ConSurf

Fix README issues

juanmirocks opened this issue · 9 comments

juanmirocks commented

(For a sample template of the desired README, see: https://github.com/Rostlab/PP2_CS_WS_2015-16/wiki/README.md-Template)

  • Write in github description very short description of what this tool does
  • Right at the beginning of the README, after the ConSurf title, write a short description and 1-3 important features of the software
  • Write who is the tool's author
  • Is bioSequence@tauex.tau.ac.il the contact person? I thought now it would be the rostlab. In any case, instead of writing an email, refer to the repo issues link.
  • [ ] Instructions like "download SwissProt and TrEMBL databases" are very difficult to carry on. Where do I download that from? Which format? ... Same with "format the databases for Blast search" or many other examples. Please always write very simple specific actions for each item, written for a 5 year old.
  • Provide specific instructions on how to download SWISSPROT or UNIPROT databases
  • [x] When you write sth like "update the location of /biodb/BLAST/Proteins/swissprot", which file structure are you assuming? You didn't yet tell any instructions or info about the environment. I guess you mean all the locations written in the CONSURF_CONSTANTS.pm file. In that case it's all fine 🌞
  • Where can I download ClustalW exactly from? Put the link and version directly (if one is required or just write latest) in the README. If I go to ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ I see latest version is now 2.`
  • Did you make it run downloading SwissProt and Treml? Is that not too much to ask?
  • [ ] I don't fine the file ConSurf.pl nor ConSurf -- do I have to generate it? -- I only find (consurf which points to ConSurf.pl)
  • Be consistent: is it the callable script consurf or ConSurf or ConSurf.pl ? You use these different casings in different examples
juanmirocks commented

@GrimSmiler please check remaining issues

GrimSmiler commented

Understood. will change update the ReadMe

juanmirocks commented

This may be of help for you to document howto download databases. Please double check

https://github.com/Rostlab/SNAP2

GrimSmiler commented

added the shell commands to download and unzip the DBs

GrimSmiler commented

may i close this issue now?

juanmirocks commented

No. I just reviewed the README, and still the issue of different casing for the program persists. Did you commit?

GrimSmiler commented

Updated the readme. Now all program calls in code snippets start with consurf. in cd ConSurf -> ConSurf is the name of the directory

GrimSmiler commented

issue closed?

juanmirocks commented

Seems good 👍