metamorpheus initial commit #587

jj-umn · 2021-05-04T19:52:32Z

Add galaxy tools for the MetaMorpheus application.
MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability.

Add galaxy tools for the MetaMorpheus application. MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability.

jj-umn · 2021-05-04T20:02:11Z

@bernt-matthias Here's my initial commit for MetaMorpheus.

It's still a little rough and needed plenty of testing. If you are willing to help with that, making sure that it meets the need of your clients, it would be much appreciated.

I haven't implemented tools for the GlycoSearchTask or the XLSearchTask as yet. I also want to check out using MetaMorpheus for Neoantigen HLA-bound searching: https://github.com/smith-chem-wisc/MetaMorpheus/wiki/1_New-Task:-Non-specific-cleavage-(%22No-Enzyme%22,-%22Non-specific%22)-searches

bernt-matthias

Hey @jj-umn. This looks great.

If you like I could ask my colleague who was interested to test this.

bernt-matthias · 2021-05-04T20:19:49Z

tools/metamorpheus/metamorpheus_calibration.xml

@@ -0,0 +1,65 @@
+<tool id="metamorpheus_calibration" name="MetaMorpeus Calibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">


Suggested change

<tool id="metamorpheus_calibration" name="MetaMorpeus Calibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">

<tool id="metamorpheus_calibration" name="MetaMorpeus Calibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">

bernt-matthias · 2021-05-04T20:26:41Z

tools/metamorpheus/macros.xml

+]]></token>
+
+    <xml name="dissociation_options">
+                    <option value="Any">Any</option>


Can you fix indentation here?

bernt-matthias · 2021-05-04T20:29:55Z

tools/metamorpheus/macros.xml

+[CommonParameters]
+TaskDescriptor = "CalibrateTask"
+MaxThreadsToUsePerFile = 11
+#if $common.set_common == 'yes' 


I would prefer to use sections instead of conditionals. Then you may skip this if-else and just use the defaults in the tool form (I guess they are the same anyway).

The disadvantage of conditionals is that they can not be changed in workflows.

Also we would know if there are no typos in the code that is currently in the if branch and the sytnax is correct (ie accepted by MM).

These config yaml files may change by the version. They can be generated with metamorpheus -g, so if possible, it might be worth adding a test to make sure the default parameters and parameter names haven't changed since the last version.

bernt-matthias · 2021-05-04T20:31:47Z

tools/metamorpheus/macros.xml

+MS3ChildScanDissociationType = "Unknown"
+#end if
+    </token>
+    <xml name="mods_params">


Is this needed?

bernt-matthias · 2021-05-04T20:35:59Z

tools/metamorpheus/macros.xml

+        </requirements>
+    </xml>
+
+    <token name="@DEFAULT_COMMON_TOML@">


What is the idea of this toml file? There seems to be some intersections with the others? Should the parameters be configurable?

bernt-matthias · 2021-05-04T20:40:06Z

tools/metamorpheus/macros.xml

+            #set $m = $re.match('^(\[.+\])$', $entry)
+            #if $m:
+                #set $category = $m.groups()[0]
+                #if $category not in $config['categories']:


I think #if $category not in $config should work, i.e. it should not be necessary to store the categories in $config['categories'].

bernt-matthias · 2021-05-04T20:43:19Z

tools/metamorpheus/macros.xml

+]]></token>
+
+    <token name="@MERGE_TOMLS@"><![CDATA[
+#def merge_tomls($tomls, $merged):


I only checked the code roughly. Can you tell we how does this differs from just concatenating the files.

bernt-matthias · 2021-05-04T20:44:39Z

tools/metamorpheus/metamorpheus_calibration.xml

+        <expand macro="calibrated_outputs"/>
+    </outputs>
+    <tests>
+        <test>


can you add expect_num_outputs .. which is always a good idea if there are outputs with filters.

bernt-matthias

Tests are not running because .shed.yml is missing.

jj-umn · 2021-05-04T21:27:24Z

@bernt-matthias I suspect the tests will now fail because the toml datatype has only made it to the dev branch.

bernt-matthias · 2021-05-05T07:09:35Z

I suspect the tests will now fail because the toml datatype has only made it to the dev branch.

True. I think the 21.05 branch will become available today. Then we can adapt the pr workflow.

Then we should also use profile 21.05.

Add profile 21.05 for toml datatype Fix metamorpheus_calibration.xml test output element name

bernt-matthias · 2021-05-06T08:11:30Z

@jj-umn just added 21.05 support for this repo: #589 .. if you merge/rebase with master tests should run.

bernt-matthias · 2021-05-06T09:22:41Z

Seems that MM tries to access a missing file / write to the installation dir.

Unhandled exception. System.UnauthorizedAccessException: Access to the path '/usr/local/lib/dotnet/tools/metamorpheus/CustomAminoAcids' is denied.
 ---> System.IO.IOException: Permission denied
   --- End of inner exception stack trace ---
   at System.IO.FileSystem.CreateDirectory(String fullPath)
   at System.IO.Directory.CreateDirectory(String path)
   at EngineLayer.GlobalVariables.WriteAminoAcidsFile()
   at EngineLayer.GlobalVariables.LoadCustomAminoAcids()
   at EngineLayer.GlobalVariables.SetUpGlobalVariables()
   at MetaMorpheusCommandLine.Program.Run(CommandLineSettings settings)
   at MetaMorpheusCommandLine.Program.<>c__DisplayClass3_0.<Main>b__1(CommandLineSettings options)
   at CommandLine.ParserResultExtensions.WithParsed[T](ParserResult`1 result, Action`1 action)
   at MetaMorpheusCommandLine.Program.Main(String[] args)
/usr/local/bin/metamorpheus: line 3:    12 Aborted                 (core dumped) dotnet $DOTNET_TOOLS/metamorpheus/CMD.dll $@

jj-umn · 2021-05-06T12:58:51Z

@bernt-matthias @bgruening @acesnik
I think MetaMorpheus has option:
--mmsettings [Optional] Path to MetaMorpheus settings
To solve that issue. I'll check into adding it to the galaxy tools.

Add --mmsettings option to prevent attempts to write to install code directory

…into metamorpheus

bernt-matthias · 2021-05-12T10:18:47Z

We will need a fatal_oom stdio regexp for Run failed, Exception: Exception of type 'System.OutOfMemoryException' was thrown. (e.g. just OutOfMemoryException). .. appears on stdout

Don't expect exact number of reported datapoints

MetaMorpheus param fixes - need double quotes around string types

bernt-matthias · 2021-08-05T07:57:50Z

Good hints here: smith-chem-wisc/MetaMorpheus#2054

bernt-matthias · 2022-03-23T16:37:47Z

FYI smith-chem-wisc/MetaMorpheus#2054 (comment)

metamorpheus initial commit

6e86fac

Add galaxy tools for the MetaMorpheus application. MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability.

jj-umn added the wip label May 4, 2021

bernt-matthias reviewed May 4, 2021

View reviewed changes

Create .shed.yml

48d3dfd

Add profile 21.05 for toml datatype

775042a

Add profile 21.05 for toml datatype Fix metamorpheus_calibration.xml test output element name

Merge branch 'master' into metamorpheus

5bb772f

jj-umn added 2 commits May 11, 2021 08:34

Add mmsettings option

7c57a8a

Add --mmsettings option to prevent attempts to write to install code directory

Merge branch 'metamorpheus' of https://github.com/jj-umn/tools-galaxyp …

d7af9ee

…into metamorpheus

bernt-matthias mentioned this pull request May 12, 2021

SG 4.0.33 & PS 2.0.25 #594

Merged

jj-umn added 2 commits May 12, 2021 08:26

Update metamorpheus_calibration.xml

7a40b99

Don't expect exact number of reported datapoints

MetaMorpheus param fixes

4c292fe

MetaMorpheus param fixes - need double quotes around string types

bernt-matthias mentioned this pull request Aug 5, 2021

MetaMorpheus toml definitions smith-chem-wisc/MetaMorpheus#2054

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metamorpheus initial commit #587

metamorpheus initial commit #587

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bernt-matthias commented Mar 23, 2022

		@@ -0,0 +1,65 @@
		<tool id="metamorpheus_calibration" name="MetaMorpeus Calibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">

metamorpheus initial commit #587

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metamorpheus initial commit #587

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