annotate old/README.rst @ 1:c0ea43315baf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
author bgruening
date Wed, 02 Oct 2019 04:31:23 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
1 Galaxy wrappers for salmon
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
2 =====================================
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
3
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
4 These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors.
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
5 All rights reserved. See the licence text below.
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
6
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
7 Currently tested with salmon 0.11.2.
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
8
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
9
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
10 Automated Installation
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
11 ======================
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
12
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
13 Galaxy should be able to automatically install the salmon for you if you have Conda dependency management enabled in Galaxy.
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
14 For more information please read the documentation at: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/conda_faq.rst
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
15
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
16
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
17 History
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
18 =======
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
19
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
20 ======== ======================================================================
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
21 Version Changes
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
22 -------- ----------------------------------------------------------------------
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
23 v0.6.3.0 - First release
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
24 -------- ----------------------------------------------------------------------
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
25 v0.7.2 - Second release
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
26 -------- ----------------------------------------------------------------------
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
27 v0.8.2 - Third release
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
28 -------- ----------------------------------------------------------------------
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
29 v0.9.1 - Fourth release
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
30 -------- ----------------------------------------------------------------------
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
31 v0.11.2 - Fifth release
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
32
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
33 ======== ======================================================================
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
34
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
35
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
36 Bug Reports
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
37 ===========
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
38
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
39 You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
40 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
41
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
42
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
43 Licence (MIT)
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
44 =============
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
45
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
46 Permission is hereby granted, free of charge, to any person obtaining a copy
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
47 of this software and associated documentation files (the "Software"), to deal
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
48 in the Software without restriction, including without limitation the rights
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
49 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
50 copies of the Software, and to permit persons to whom the Software is
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
51 furnished to do so, subject to the following conditions:
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
52
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
53 The above copyright notice and this permission notice shall be included in
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
54 all copies or substantial portions of the Software.
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
55
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
56 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
57 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
58 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
59 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
60 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
61 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
c0ea43315baf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
diff changeset
62 THE SOFTWARE.