From 81da89dd3e5d878eb0940563bc0c4bb6baf3eeeb Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 18 Mar 2022 11:58:50 +1100 Subject: [PATCH 1/2] Add a check for fastANI Add a check for fastANI to prevent running of loop and echoing of messages that indicate the job is being successfully run --- scripts/fastani_with_slurm.sh | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/scripts/fastani_with_slurm.sh b/scripts/fastani_with_slurm.sh index c3b0aed..fa35a6b 100755 --- a/scripts/fastani_with_slurm.sh +++ b/scripts/fastani_with_slurm.sh @@ -14,6 +14,15 @@ # more details. You should have received a copy of the GNU General Public License along with # Bacsort. If not, see . +# Check for fastANI +if command -v fastANI >/dev/null 2>&1 ; then + echo "fastANI found" + echo "version: $(fastANI -v)" +else + echo "Error: fastANI not found - please install fastANI and try again" + exit +fi + group_count=32 mkdir -p tree From 3ed6e98a006262e65f5e6a85ec4f7d8eb23c2460 Mon Sep 17 00:00:00 2001 From: Max Cummins Date: Fri, 18 Mar 2022 12:00:18 +1100 Subject: [PATCH 2/2] Add a dependency check for fastANI Add a dependency check for fastANI to prevent loop being run anyway and messages indicating the job is running --- scripts/fastani_in_parallel.sh | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/scripts/fastani_in_parallel.sh b/scripts/fastani_in_parallel.sh index ffa4669..b7a95d2 100755 --- a/scripts/fastani_in_parallel.sh +++ b/scripts/fastani_in_parallel.sh @@ -14,6 +14,15 @@ # more details. You should have received a copy of the GNU General Public License along with # Bacsort. If not, see . +# Check for fastANI +if command -v fastANI >/dev/null 2>&1 ; then + echo "fastANI found" + echo "version: $(fastANI -v)" +else + echo "Error: fastANI not found - please install fastANI and try again" + exit +fi + mkdir -p tree printf "\n"