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SG 4.0.33 & PS 2.0.25 #594

Merged
merged 15 commits into from
May 21, 2021
Merged

SG 4.0.33 & PS 2.0.25 #594

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1cb5fbd
bump peptideshaker and searchgui
bernt-matthias Apr 22, 2021
d8d9887
use new option use_log_folder
bernt-matthias Apr 22, 2021
5dba6bf
bump
bernt-matthias Apr 29, 2021
793749d
bump
bernt-matthias Apr 29, 2021
1b45a18
SG 4.0.33
CarlosHorro May 12, 2021
e45d63b
Merge branch 'topic/bump-sg-ps-next' into sg_4033
CarlosHorro May 12, 2021
cb7d49d
In some cases, exceptions may be thrown without stopping the executio…
CarlosHorro May 19, 2021
76797b5
Better way to avoid stopping PS execution by paths.txt non-blocking e…
CarlosHorro May 19, 2021
ddbc56b
bugfix
CarlosHorro May 19, 2021
ebb12a3
Added some help information related to not using mgf files when using…
CarlosHorro May 20, 2021
13f31d6
help fix
CarlosHorro May 20, 2021
6397ea4
Added a TODO note about --exec_dir
CarlosHorro May 21, 2021
5ad2aa4
Added test files for MetaMorpheus
CarlosHorro May 21, 2021
beadf27
Added MetaMorpheus test
CarlosHorro May 21, 2021
4084728
Added some note about the source of the data for metamorpheus test
CarlosHorro May 21, 2021
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10 changes: 9 additions & 1 deletion tools/peptideshaker/fasta_cli.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,15 @@
###########################################

echo 'Creating decoy database.' &&
searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag &&
searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
--exec_dir="./bin/"
-use_log_folder 0
-temp_folder `pwd`
-in '${input_database.display_name}'
-decoy
-decoy_flag $database_processing_options.decoy_tag
-suffix $database_processing_options.decoy_type
-decoy_suffix $database_processing_options.decoy_file_tag &&
mv '${output_db_name}' output
]]>
</command>
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2 changes: 1 addition & 1 deletion tools/peptideshaker/ident_params.xml
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Expand Up @@ -30,8 +30,8 @@
#####################################################
searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
--exec_dir="./bin/"
-use_log_folder 0
-out './IdentificationParametersOutput.par'

## SPECTRUM MATCHING PARAMETERS

-frag_tol '${spectrum_matching_options.fragment_tol}'
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4 changes: 2 additions & 2 deletions tools/peptideshaker/macros_basic.xml
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Expand Up @@ -11,9 +11,9 @@
</stdio>
</xml>
<token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
<token name="@SEARCHGUI_VERSION@">4.0.25</token>
<token name="@SEARCHGUI_VERSION@">4.0.33</token>
<token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
<token name="@PEPTIDESHAKER_VERSION@">2.0.18</token>
<token name="@PEPTIDESHAKER_VERSION@">2.0.25</token>
<token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
<xml name="citations">
<citations>
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9 changes: 6 additions & 3 deletions tools/peptideshaker/peptide_shaker.xml
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Expand Up @@ -26,8 +26,6 @@
#set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
#set $bin_dir = "bin"
#set $exporting_followup_boolean = False
## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
## trap ">&2 cat resources/*.log" EXIT;

mkdir output_reports &&
cwd=`pwd` &&
Expand Down Expand Up @@ -73,7 +71,7 @@
peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
-gui 0
-temp_folder \$cwd/PeptideShakerCLI
-log \$cwd/resources
-use_log_folder 0
-reference '$exp_str'
-identification_files \$cwd/searchgui_input.zip
-id_params \$cwd/SEARCHGUI_IdentificationParameters.par
Expand Down Expand Up @@ -187,6 +185,11 @@
#end if
#end if
#end if

## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)"
## is fixed , we can avoid the process to be stopped by removing that message from the output

| grep -v "resources/conf/paths.txt (Permission denied)"

## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
#if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
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6 changes: 3 additions & 3 deletions tools/peptideshaker/searchgui.xml
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Expand Up @@ -65,6 +65,7 @@
echo 'running search gui' &&
searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
--exec_dir="\$cwd/${bin_dir}"
-use_log_folder 0
-spectrum_files \$cwd
-fasta_file "\$cwd/input_fasta_file.fasta"
-output_folder \$cwd/output
Expand Down Expand Up @@ -186,8 +187,7 @@
<option value="Tide">Tide</option>
<option value="MyriMatch">MyriMatch</option>
<option value="MS_Amanda">MS_Amanda</option>
<!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
<!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
<option value="MetaMorpheus">MetaMorpheus</option>
<!-- Windows only
<option value="Andromeda">Andromeda</option>
-->
Expand Down Expand Up @@ -324,7 +324,7 @@ Runs multiple search engines on any number of MGF peak lists using SearchGUI.

Default: X! Tandem and MS-GF+ are executed.

Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.

**Input FASTA**

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