# 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 @@ - - - - - + + + + + + + + +
+ - - - - + + + + +