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.

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

Update Cardinal Version 3.4.3 #763

Merged
merged 18 commits into from
Jul 4, 2024

Conversation

MarenStillger
Copy link
Contributor

This PR updates Cardinal to version 3.4.3.

Copy link
Collaborator

@bernt-matthias bernt-matthias left a comment

Choose a reason for hiding this comment

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

Just two technical comments from my side.

<description>spatial classification of mass spectrometry imaging data</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements">
<requirement type="package" version="2.3">r-gridextra</requirement>
<requirement type="package" version="3.3.5">r-ggplot2</requirement>
<!--requirement type="package" version="2.3">r-gridextra</requirement>
Copy link
Collaborator

Choose a reason for hiding this comment

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

We can just remove instead of comment. git stores it anyway.

Copy link
Contributor Author

Choose a reason for hiding this comment

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

thanks, updated it accordingly :)

</expand>
<command detect_errors="exit_code">
<![CDATA[
#for $i, $infile in enumerate($infiles):
#if $infile.ext == 'imzml'
ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
cp '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
Copy link
Collaborator

Choose a reason for hiding this comment

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

Is copying really necessary?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

unfortunately yes, otherwise neither imzml nor analyze75 files will be loaded

@@ -1,4 +1,4 @@
<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0">
<tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
Copy link
Member

Choose a reason for hiding this comment

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

please add also a profile="22.05" to each tool

Copy link
Contributor Author

Choose a reason for hiding this comment

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

thanks, added the profile to all tools 👍

Copy link
Member

@bgruening bgruening left a comment

Choose a reason for hiding this comment

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

Cool, thanks a lot!

@bgruening bgruening enabled auto-merge July 4, 2024 12:33
@bgruening bgruening merged commit 91e77c1 into galaxyproteomics:master Jul 4, 2024
11 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants