Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PS updated to 2.0.15 & SG updated to 4.0.22 #570

Merged
merged 16 commits into from
Mar 16, 2021
Merged

PS updated to 2.0.15 & SG updated to 4.0.22 #570

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
16 commits
Select commit Hold shift + click to select a range
17491b3
PS updated to 2.0.14
CarlosHorro Mar 11, 2021
7700dc1
Removed wrong result in test (removed from PS after last update).
CarlosHorro Mar 14, 2021
e9a71c4
Merge branch 'master' into sg_4022_ps_2014
CarlosHorro Mar 14, 2021
a254773
PS updated to 2.0.15
CarlosHorro Mar 15, 2021
a9e4f37
use_shared_home="false"
CarlosHorro Mar 15, 2021
93f1d0a
some fixes for searchgui and peptideshaker
bernt-matthias Mar 12, 2021
a6e9a89
Profile updated to 20.01
CarlosHorro Mar 15, 2021
ac36119
Added logs to stderr output.
CarlosHorro Mar 15, 2021
d7c9057
Added logs to PS stderr output.
CarlosHorro Mar 15, 2021
95736b3
detect oom errors as fatal_oom and not fatal
bernt-matthias Mar 15, 2021
7416940
Merge pull request #2 from bernt-matthias/CarlosHorro_sg_4022_ps_2014
CarlosHorro Mar 15, 2021
fe669cf
Merge branch 'master' into sg_4022_ps_2014
CarlosHorro Mar 15, 2021
48797cf
Undone some last features until app behaviour is fixed.
CarlosHorro Mar 15, 2021
2bc4ae3
Refreshing PR
CarlosHorro Mar 16, 2021
bbe7a74
Added profile 20.01 to fasta_cli and ident_params tools
CarlosHorro Mar 16, 2021
f921b21
Readded PS 20.01 profile.
CarlosHorro Mar 16, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions tools/peptideshaker/macros_basic.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,9 @@
</stdio>
</xml>
<token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
<token name="@SEARCHGUI_VERSION@">4.0.12</token>
<token name="@SEARCHGUI_VERSION@">4.0.22</token>
<token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
<token name="@PEPTIDESHAKER_VERSION@">2.0.9</token>
<token name="@PEPTIDESHAKER_VERSION@">2.0.15</token>
<token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
<xml name="citations">
<citations>
Expand Down
4 changes: 1 addition & 3 deletions tools/peptideshaker/peptide_shaker.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,7 @@
</requirements>
<expand macro="stdio" />

<command><![CDATA[
## When supporting more advanced Galaxy versions: command use_shared_home="false"
<command use_shared_home="false"><![CDATA[
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think it would be better to increase the profile of the tools to something greater than or equal to 18.01.

See https://github.com/galaxyproject/galaxy/blob/ce23f963e036722865ecd27fda509f173406ab61/lib/galaxy/tool_util/parser/xml.py#L169

I would suggest at least 20.01

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, you are right @bernt-matthias, thank you. That was something I wanted to do some time ago but I didn't remember to include it...

#from datetime import datetime
#set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
#set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
Expand Down Expand Up @@ -626,7 +625,6 @@
<has_line_matching expression="520.9862671 4666.4399414063"/>
<has_line_matching expression="267.4349976 50.7710571289"/>
<has_line_matching expression="665.7418213 3.8165459633"/>
<has_line_matching expression="672.2329102 146.2656707764"/>
<has_line_matching expression="634.7792969 2367.6374511719"/>
</assert_contents>
</element>
Expand Down