Mercurial > repos > richard-burhans > segalign
changeset 2:9e34b25a8670 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 288c3e1887d4c13dcc922c612957460471977ff0
| author | richard-burhans |
|---|---|
| date | Thu, 18 Apr 2024 17:17:12 +0000 |
| parents | d3f11ae6790c |
| children | 6f46cebc9ed8 |
| files | diagonal_partition.py macros.xml run_segalign_diagonal_partition segalign.xml |
| diffstat | 4 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/diagonal_partition.py Thu Apr 18 16:51:46 2024 +0000 +++ b/diagonal_partition.py Thu Apr 18 17:17:12 2024 +0000 @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/env python """ Diagonal partitioning for segment files output by SegAlign.
--- a/macros.xml Thu Apr 18 16:51:46 2024 +0000 +++ b/macros.xml Thu Apr 18 17:17:12 2024 +0000 @@ -7,7 +7,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.1.2.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.05</token> <xml name="edam_ontology"> <edam_operations>
--- a/run_segalign_diagonal_partition Thu Apr 18 16:51:46 2024 +0000 +++ b/run_segalign_diagonal_partition Thu Apr 18 17:17:12 2024 +0000 @@ -3,7 +3,6 @@ set -o errexit set -o nounset set -o pipefail -#set -o xtrace ## ## parse arguments
--- a/segalign.xml Thu Apr 18 16:51:46 2024 +0000 +++ b/segalign.xml Thu Apr 18 17:17:12 2024 +0000 @@ -30,7 +30,9 @@ #if str($mode.mode_selector) == "segalign" #if str($mode.diagonal_partition_options.diagonal_partition) == "true" #set $segalign_mode = "segalign_diagonal_partition" - '$__tool_directory__/run_segalign_diagonal_partition' + ## explicitly calling bash to bypass a pulsar bug + ## https://github.com/galaxyproject/pulsar/issues/341 + bash '$__tool_directory__/run_segalign_diagonal_partition' --tool_directory '$__tool_directory__' --max_segments '$mode.diagonal_partition_options.max_segments' #else