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Detects OOM for CellBrowser even if tool exits with 0 code. #296

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merged 3 commits into from
Jul 15, 2023
Merged

Detects OOM for CellBrowser even if tool exits with 0 code. #296

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f65337f
Detects OOM for CellBrowser even if tool exits with 0 code.
pcm32 Jul 5, 2023
73ea740
Bumps galaxy build
pcm32 Jul 5, 2023
5a07e3e
Try to fix test retrieval
pcm32 Jul 15, 2023
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3 changes: 2 additions & 1 deletion tools/tertiary-analysis/ucsc-cell-browser/cell-browser.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="1.0.0+galaxy0" profile="18.01">
<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="1.0.0+galaxy1" profile="18.01">
<description>displays single-cell clusterized data in an interactive web application.</description>
<requirements>
<requirement type="package" version="1.0.0">ucsc-cell-browser</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
<regex source="both" match="Killed" level="fatal_oom" description="Killed, most likely due to OOM" />
</stdio>
<command><![CDATA[
#if $input_type.expression_source == "native-cell-browser":
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1 change: 1 addition & 0 deletions tools/tertiary-analysis/ucsc-cell-browser/get_test_data.sh
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@@ -1,3 +1,4 @@
#!/usr/bin/env bash
wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.project.h5ad
mkdir -p test-data
mv E-MTAB-6077.project.h5ad test-data/
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