Resfinder download should not use tar wildcards, broken in busybox #494

soedinglab · Oct 14, 2021 · 56816b3 · 56816b3
1 parent e85ceb9
commit 56816b3
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/data/workflow/databases.sh b/data/workflow/databases.sh
@@ -223,8 +223,11 @@ case "${SELECTION}" in
         if notExists "${TMP_PATH}/download.done"; then
             downloadFile "https://api.bitbucket.org/2.0/repositories/genomicepidemiology/resfinder_db/commit/master?fields=hash,date" "${TMP_PATH}/version"
             downloadFile "https://bitbucket.org/genomicepidemiology/resfinder_db/get/master.tar.gz" "${TMP_PATH}/master.tar.gz"
-            tar -C "${TMP_PATH}" --strip-components=1 -xzvf "${TMP_PATH}/master.tar.gz" "*.fsa"
-            rm -f "${TMP_PATH}/master.tar.gz"
+            # avoid tar wildcard extraction as it's not available in busybox tar (windows, biocontainer)
+            mkdir -p "${TMP_PATH}/fsa"
+            tar -C "${TMP_PATH}/fsa" --strip-components=1 -xzvf "${TMP_PATH}/master.tar.gz"
+            mv -f -- "${TMP_PATH}/fsa/"*.fsa "${TMP_PATH}"
+            rm -rf -- "${TMP_PATH}/master.tar.gz" "${TMP_PATH}/fsa"
             touch "${TMP_PATH}/download.done"
         fi
         INPUT_TYPE="FSA"