made isilonmount location dependent on chaparone machine

molgenis · Sep 11, 2024 · f39ddd8 · f39ddd8
1 parent b213726
commit f39ddd8
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Showing 6 changed files with 6 additions and 3 deletions.
diff --git a/bin/ParseDarwinSamplesheet.sh b/bin/ParseDarwinSamplesheet.sh
@@ -2,7 +2,6 @@
 
 # executed by the umcg-gd-ateambot, part of the ConcordanceCheck.
 
-
 if [[ "${BASH_VERSINFO[0]}" -lt 4 ]]
 then
 	echo "Sorry, you need at least bash 4.x to use ${0}." >&2

diff --git a/bin/copyConcordanceCheckData.sh b/bin/copyConcordanceCheckData.sh
@@ -243,7 +243,7 @@ else
 			while IFS= read -r i
 			do
 				fileName=$(basename "${i}")
-				printf '\\\\zkh\\appdata\\medgen\\leucinezipper%s\r\n' "${i//\//${windowsPathDelimeter}}" > "${fileName}"
+				printf "${ISILON_MOUNTPOINT}%s\r\n" "${i//\//${windowsPathDelimeter}}" > "${fileName}"
 			done < <(find "${PRM_ROOT_DIR}/concordance/results/" -maxdepth 1 -type f -iname "${filePrefix}.*")
 			# shellcheck disable=SC2029
 			ssh "${DATA_MANAGER}@${HOSTNAME_TMP}" "mv \"${sampleSheet}\" \"${TMP_ROOT_DIAGNOSTICS_DIR}/concordance/samplesheets/archive/\""

diff --git a/check/shellcheck.sh b/check/shellcheck.sh
@@ -75,6 +75,7 @@ MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
 #  * Includes sourced files, so the libraries from the lib/ subfolder 
 #    are checked too as long a they are used in at least one script.
 #
+CIRCLECI=true
 if [[ "${CIRCLECI:-}" == true ]]
 then
 	#
@@ -88,4 +89,4 @@ then
 	#
 	export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2312"
 fi
-shellcheck -a -x -o all -f "${format}" "${MYDIR}"/../bin/*.sh | sed "s|${MYDIR}/../||g"
+shellcheck -a -x -o all -f "${format}" "${MYDIR}"/../bin/*.sh | sed "s|${MYDIR}/../||g"
diff --git a/etc/upzkh1054.cfg b/etc/upzkh1054.cfg
@@ -4,5 +4,6 @@ SCR_LFS='${TMP_LFS}'
 HOSTNAME_PRM='localhost'
 DIAGNOSTICS_TMP_LFS='tmp07'
 HOSTNAME_TMP='wh-porch+wingedhelix'
+ISILON_MOUNTPOINT='\\\\zkh\\appdata\\medgen\\wingedhelix'
 DAT_LFS='dat07'
 TMP_ROOT_DIAGNOSTICS_DIR="/groups/${GROUP}/${TMP_LFS}/"
diff --git a/etc/upzkh1055.cfg b/etc/upzkh1055.cfg
@@ -3,6 +3,7 @@ PRM_LFS='prm05'
 SCR_LFS='${TMP_LFS}'
 HOSTNAME_PRM='localhost'
 DIAGNOSTICS_TMP_LFS='tmp05'
+ISILON_MOUNTPOINT='\\\\zkh\\appdata\\medgen\\zincfinger'
 HOSTNAME_TMP='bb-porch+betabarrel'
 DAT_LFS='dat05'
 TMP_ROOT_DIAGNOSTICS_DIR="/groups/${GROUP}/${TMP_LFS}/"
diff --git a/etc/upzkh1056.cfg b/etc/upzkh1056.cfg
@@ -3,6 +3,7 @@ PRM_LFS='prm06'
 SCR_LFS='${TMP_LFS}'
 HOSTNAME_PRM='localhost'
 DIAGNOSTICS_TMP_LFS='tmp06'
+ISILON_MOUNTPOINT='\\\\zkh\\appdata\\medgen\\leucinezipper'
 HOSTNAME_TMP='cf-porch+copperfist'
 DAT_LFS='dat06'
 TMP_ROOT_DIAGNOSTICS_DIR="/groups/${GROUP}/${TMP_LFS}/"
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,6 @@ @@
     # executed by the umcg-gd-ateambot, part of the ConcordanceCheck.
     if [[ "${BASH_VERSINFO[0]}" -lt 4 ]]
     then
     	echo "Sorry, you need at least bash 4.x to use ${0}." >&2
@@ Expand Down @@