galaxyproject / cargo-port

cache packages permanently
https://depot.galaxyproject.org/software/
MIT License
12 stars 34 forks source link

added gem-library #167

Closed lldelisle closed 4 years ago

lldelisle commented 4 years ago

Hi, This is the first time I am using cargo-port...

  1. For the url, I just click right on the sourgeforge webpage to get the url. When I do wget I see different URL:
    
    [ldelisle@helvetios softwares]$ wget https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2/download
    --2020-02-10 11:30:02--  https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2/download
    Resolving scitassrv9.epfl.ch (scitassrv9.epfl.ch)... 128.178.209.216
    Connecting to scitassrv9.epfl.ch (scitassrv9.epfl.ch)|128.178.209.216|:80... connected.
    Proxy request sent, awaiting response... 302 Found
    Location: https://downloads.sourceforge.net/project/gemlibrary/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2?r=&ts=1581330603&use_mirror=liquidtelecom [following]
    --2020-02-10 11:30:03--  https://downloads.sourceforge.net/project/gemlibrary/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2?r=&ts=1581330603&use_mirror=liquidtelecom
    Connecting to scitassrv9.epfl.ch (scitassrv9.epfl.ch)|128.178.209.216|:80... connected.
    Proxy request sent, awaiting response... 302 Found
    Location: https://liquidtelecom.dl.sourceforge.net/project/gemlibrary/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2 [following]
    --2020-02-10 11:30:04--  https://liquidtelecom.dl.sourceforge.net/project/gemlibrary/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2
    Connecting to scitassrv9.epfl.ch (scitassrv9.epfl.ch)|128.178.209.216|:80... connected.
    Proxy request sent, awaiting response... 200 OK
    Length: 33847526 (32M) [application/octet-stream]
    Saving to: ‘download’

100%[=====================================================================================================================================================================================================================================>] 33,847,526 8.45MB/s in 4.7s

2020-02-10 11:30:10 (6.87 MB/s) - ‘download’ saved [33847526/33847526]

2. I am not sure I understood the last column of the file... I put false but maybe it should have been True (sourceforge did not ask to stop download, we are more afraid that the url is not stable)...
3. To get the license, I need to download and then run:
`GEM-binaries-Linux-x86_64-core_i3-20130406-045632/bin/gem-mappability --show-license`.
Here is the result:

Welcome to GEM-mappability build 1.315 (beta) - (2013/03/29 02:59:40 GMT) (c) 2008-2013 Paolo Ribeca paolo.ribeca@gmail.com (c) 2010-2013 Santiago Marco Sola santiagomsola@gmail.com (c) 2010-2013 Leonor Frias Moya leonor.frias@gmail.com For the terms of use, run the program with the option --show-license.


This software is copyright (C) 2008-2010 Centre de Regulació Genòmica, Barcelona, Spain (CRG) (C) 2010-2012 Centro Nacional de Análisis Genómico, Barcelona, Spain (CNAG) Parc Científic de Barcelona, Spain (PCB) and was developed by the following authors: (C) 2008-2012 Paolo Ribeca paolo.ribeca@gmail.com (CRG, CNAG) (C) 2010-2012 Santiago Marco Sola santiagomsola@gmail.com (CNAG) (C) 2010-2012 Leonor Frias Moya leonor.frias@gmail.com (CNAG)

===================================== The GEM non-commercial binary license

If you use the software, you accept this license. If you do not accept the license, do not use the software.

The present license grants you the right to freely use for any purpose this binary and all the results it generates, provided that the binary is not embedded in a commercial software suite. That is: you may freely use the program either as a standalone application or integrated into a larger non-commercial software environment, but you may not use it (regardless of the way you obtained it) as a component of a commercial system. If you realize that the software is being run in violation of this rule, you must immediately stop using it and notify genome.multitool.legal@gmail.com of the violation.

The present license also grants you the right to freely redistribute exact copies of this binary for any non-commercial purpose. In particular: (1) you may not embed it into, or allow it to be executed from, a commercial software suite (that is: you may redistribute the program either as a standalone application or integrated into a larger non-commercial software environment, but not as a component of a commercial system) (2) you may not sell, rent, lease or lend the software (3) you may not modify, reverse engineer, decompile or disassemble the software (4) you must retain all copyright, patent, trademark, and attribution notices that are present in the software, including this license (5) you may not misrepresent the origin of the software, and the material you distribute must fairly acknowledge the presence of the software with prominent notices.

Uses other than those explicitly allowed in this document require separate licensing agreement from the copyright holders. In case of any doubt, please contact paolo.ribeca@gmail.com.

THE PROGRAM IS PROVIDED "AS IS", WITHOUT ANY WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED, IN THE HOPE THAT IT WILL BE USEFUL; THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE ENTIRE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

bgruening commented 4 years ago

The present license also grants you the right to freely redistribute exact copies of this binary for any non-commercial purpose.

I think this is fine for us. But please note that if you use this in a Galaxy wrapper, you probably need to ask the user if its for non-commercial use.

The False also looks like it, as Sourceforge is unstable in regards to URLs.

bgruening commented 4 years ago

Still want to merge it?

lldelisle commented 4 years ago

I guess I can I ask the owner for putting it in galaxy + bioconda, right? Maybe we can wait its answer...

bgruening commented 4 years ago

I guess I can I ask the owner for putting it in galaxy + bioconda, right?

Yes sure, but make sure that you make clear that a Galaxy admin can not know if a user is commercial or not. Its a public server that we need to assume.

lldelisle commented 4 years ago

Yes, I will do like for the MEME suite in tools-iuc (check box + warning in the help). Thank you very much for pointing this.

lldelisle commented 4 years ago

Apparently, the owner is going to make available a new version on a "stable" url... Thanks