Fix README issues - Githubissues

juanmirocks commented 8 years ago

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

[x] Write in github description very short description of what this tool does
[x] Right at the beginning of the README, after the ConSurf title, write a short description and 1-3 important features of the software
[x] Write who is the tool's author
[x] 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.
[x] 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 :sun_with_face:
[x] 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.`
[x] 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)~~
[x] Be consistent: is it the callable script consurf or ConSurf or ConSurf.pl ? You use these different casings in different examples

juanmirocks commented 8 years ago

@GrimSmiler please check remaining issues

GrimSmiler commented 8 years ago

Understood. will change update the ReadMe

juanmirocks commented 8 years ago

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

https://github.com/Rostlab/SNAP2

GrimSmiler commented 8 years ago

added the shell commands to download and unzip the DBs

GrimSmiler commented 8 years ago

may i close this issue now?

juanmirocks commented 8 years ago

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

GrimSmiler commented 8 years ago

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 8 years ago

issue closed?

juanmirocks commented 8 years ago

Seems good :+1:

Rostlab / ConSurf

Fix README issues #9