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Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

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Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

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d5b2dcd
Fix up tool_data_table_conf files
pvanheus Feb 22, 2025
a26b512
Remember to save this time
pvanheus Feb 22, 2025
ef8d97b
Fix columns in test-data
pvanheus Feb 22, 2025
e44d3cd
Correct tool data table name
pvanheus Feb 26, 2025
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2 changes: 1 addition & 1 deletion tools/artic/artic_minion.xml
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@@ -1,4 +1,4 @@
<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy0" profile="20.09">
<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy1" profile="23.2">
<description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/artic/test-data/clair3_models.loc
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Expand Up @@ -7,4 +7,4 @@
#
#So, clair3_models.loc could look something like this:
test_model ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3
r1041_e82_400bps_sup_v500 r1041_e82_400bps_sup_v500 ont 01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678 /no/such/model rerio
r1041_e82_400bps_sup_v500 ont 01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678 /no/such/model rerio
11 changes: 1 addition & 10 deletions tools/artic/tool-data/models.loc.sample
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@@ -1,13 +1,4 @@
#Enter the model names in the second column, the platform name in the second and the path in the third.
#This file lists the locations and dbkeys of all the model files
#under the "models" directory (a directory that contains a directory
#for each build). This file has the format (white space characters are
#TAB characters):
#
#<id> <name> <platform> <path>
#
#So, all_model.loc could look something like this:
test_model "the_model_name" r941_prom_hac_g360+g422 $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422#This file lists the names and locations of all the clair3 model files
#This file lists the names and locations of all the clair3 model files
#under the "clair3_models" directory (a directory that contains a directory
#for each build). This file has the format (white space characters are
#TAB characters):
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2 changes: 1 addition & 1 deletion tools/clair3/clair3.xml
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Expand Up @@ -2,7 +2,7 @@
<description>germline small variant caller for long-reads</description>
<macros>
<token name="@TOOL_VERSION@">1.0.10</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<xrefs>
<xref type='bio.tools'>clair3</xref>
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13 changes: 6 additions & 7 deletions tools/clair3/test-data/clair3_models.loc
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@@ -1,11 +1,10 @@
#Enter the model names in the second column, the platform name in the second and the path in the third.
#This file lists the locations and dbkeys of all the model files
#under the "models" directory (a directory that contains a directory
#This file lists the names and locations of all the clair3 model files
#under the "clair3_models" directory (a directory that contains a directory
#for each build). This file has the format (white space characters are
#TAB characters):
#
#<unique_build_id> <display_name> <platform> <file_path> <source>
#<unique_name> <platform> <sha256sum> <file_path> <source>
#
#So, all_model.loc could look something like this:
test_model "the_model_name" ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3
r1041_e82_400bps_sup_v500 r1041_e82_400bps_sup_v500 ont /no/such/model rerio
#So, clair3_models.loc could look something like this:
test_model ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3
r1041_e82_400bps_sup_v500 ont 01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678 /no/such/model rerio
9 changes: 9 additions & 0 deletions tools/clair3/tool-data/clair3_models.loc.sample
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@@ -0,0 +1,9 @@
#This file lists the names and locations of all the clair3 model files
#under the "clair3_models" directory (a directory that contains a directory
#for each build). This file has the format (white space characters are
#TAB characters):
#
#<unique_name> <platform> <sha256sum> <file_path> <source>
#
#So, clair3_models.loc could look something like this:
test_model ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3
11 changes: 0 additions & 11 deletions tools/clair3/tool-data/model.loc.sample
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6 changes: 3 additions & 3 deletions tools/clair3/tool_data_table_conf.xml.sample
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<?xml version="1.0"?>
<tables>
<!-- Locations of clair3 model folders -->
<table name="model" comment_char="#">
<columns>value, name, platform, path, source</columns>
<file path="tool-data/model.loc" />
<table name="clair3_models" comment_char="#">
<columns>value, platform, sha256, path, source</columns>
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That's very unfortunate, but you cannot change the columns of an existing data table.
You need also a new table name now.

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@pvanheus pvanheus Feb 24, 2025 •
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Just to clarify - the table is not like the one described here - the canonical version of the table is the one described here: #6659 (there was something to create the table before this DM was created, even though it was referenced in the clair3 tool). So this brings the clair3 copy of the data table definition in line with the one made by the data manager.

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Ah ok, I see (was wondering how I had missed this when reviewing the PR for the DM). Then this might work.
Not exactly sure how all the different versions of this file are treated by Galaxy though.

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Not exactly sure how all the different versions of this file are treated by Galaxy though.

This will create problems if someone already installed the version without the fix.

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@bernt-matthias will the problem be there if people installed the tool with the older version of the data table or only for those installing the DM (if, for example, a data table changed after the DM was installled)?

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Yeah, but I guess/hope we can manage to clean things up.

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but @bernt-matthias you'd merge without a version bump then, correct?

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Yes.

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@wm75 wm75 Feb 26, 2025 •
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ok, then let's do that. @pvanheus can you undo the two wrapper version bumps and I'll try to sort out the EU data tables?

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@wm75 wm75 Feb 26, 2025 •
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It also seems that you haven't captured all the changes from #6796 (which unfortunately has been merged already) in this PR here (which means we cannot overwrite the +galaxy0 version of artic_minion here anymore). Can you please just rebase?

(No harm done with the artic_minion tool since that one always had the correct tool_data_table_conf data :-) but rebasing would still be good to make the situation less confusing. )

<file path="tool-data/clair3_models.loc" />
</table>
<table name="all_fasta" comment_char="#">
<columns>value, dbkey, name, path</columns>
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4 changes: 2 additions & 2 deletions tools/clair3/tool_data_table_conf.xml.test
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@@ -1,8 +1,8 @@
<?xml version="1.0"?>
<tables>
<!-- Locations of model folders -->
<!-- Locations of clair3 model folders -->
<table name="clair3_models" comment_char="#">
<columns>value, name, platform, path, source</columns>
<columns>value, platform, sha256, path, source</columns>
<file path="${__HERE__}/test-data/clair3_models.loc" />
</table>
<!-- Locations of reference genome files in fasta format -->
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