# HG changeset patch
# User iuc
# Date 1758720596 0
# Node ID 5fe428757fabd80c88d96e5c9648f26f0d3b15e2
# Parent 04036a60676bf7cf0b3cefef4295bd7aa5c262a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit a23e39116e96db7282fa796a10e131bb2d91218b
diff -r 04036a60676b -r 5fe428757fab macros.xml
--- a/macros.xml Wed Jun 04 09:08:30 2025 +0000
+++ b/macros.xml Wed Sep 24 13:29:56 2025 +0000
@@ -6,7 +6,7 @@
0.5.5
- 1
+ 2
21.05
diff -r 04036a60676b -r 5fe428757fab ncbi_fcs_gx.xml
--- a/ncbi_fcs_gx.xml Wed Jun 04 09:08:30 2025 +0000
+++ b/ncbi_fcs_gx.xml Wed Sep 24 13:29:56 2025 +0000
@@ -11,13 +11,14 @@
#if $mode.config_tag.fields.use_source_manifest == "1"
#set manifest_pathname = $mode.config_tag.fields.source_manifest
#end if
+ GX_DB_DIR="\${TMPDIR}/$mode.config_tag" &&
## skip checksumming the database if the db_state_file exists
- if [ ! -e "\${TMPDIR}/sync-files-completed.txt" ]; then
+ if [ ! -e "\${GX_DB_DIR}/sync-files-completed.txt" ]; then
## copy data to local storage
- mkdir -p "\${TMPDIR}" &&
- sync_files.py get --mft '$manifest_pathname' --dir "\${TMPDIR}" > sync_files.log 2>&1 ||
+ mkdir -p "\${GX_DB_DIR}" &&
+ sync_files.py get --mft '$manifest_pathname' --dir "\${GX_DB_DIR}" > sync_files.log 2>&1 ||
{ cat sync_files.log >&2 ; false ; } &&
- touch "\${TMPDIR}/sync-files-completed.txt";
+ touch "\${GX_DB_DIR}/sync-files-completed.txt";
fi &&
## run gx
GX_NUM_CORES=\${GALAXY_SLOTS:-2} run_gx.py
@@ -41,7 +42,7 @@
#if $mode.screen_adv.ignore_same_kingdom
--ignore-same-kingdom
#end if
- --gx-db "\${TMPDIR}"
+ --gx-db "\${GX_DB_DIR}"
--out-basename output
--action-report true
--generate-logfile false
@@ -143,19 +144,25 @@
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-
-
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