Add cog-publish-link.sh for repointing latest

bin/control/cog-publish-link.sh

@@ -0,0 +1,34 @@
+set -euo pipefail
+
+# Repoint latest
+# This script is usually run automatically by cog-publish
+# Under exceptional circumstances one may need to repoint the latest data set manually
+#
+# Usage:
+#   cog-publish-link.sh <DATESTAMP>
+#
+# $1 DATESTAMP that latest should link to
+
+chmod 755 $COG_PUBLISHED_DIR/$1/
+ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta $COG_PUBLISHED_DIR/elan.latest.consensus.fasta
+ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta.fai $COG_PUBLISHED_DIR/elan.latest.consensus.fasta.fai
+ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.tsv $COG_PUBLISHED_DIR/majora.latest.metadata.tsv
+ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.matched.fasta $COG_PUBLISHED_DIR/elan.latest.consensus.matched.fasta
+ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.matched.tsv $COG_PUBLISHED_DIR/majora.latest.metadata.matched.tsv
+
+# NOTE samstudio8 2021-01-28
+#      https://github.com/SamStudio8/elan-nextflow/issues/12
+#      We've now moved away from providing symlinks at a daily resolution because
+#      its hilariously expensive to maintain them and nobody actually uses them.
+#      latest/ is now a real dir rather than a symlink. To match the expected
+#      behaviour of the latest files being accessible via latest/ we'll additionally
+#      now symlink the FASTA and TSV. Eventually we can deprecate providing them
+#      above this dir.
+#      I now use a `head` symlink to keep track of the last successful run.
+ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta $COG_PUBLISHED_DIR/latest/elan.consensus.fasta
+ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta.fai $COG_PUBLISHED_DIR/latest/elan.consensus.fasta.fai
+ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.tsv $COG_PUBLISHED_DIR/latest/majora.metadata.tsv
+ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.matched.fasta $COG_PUBLISHED_DIR/latest/elan.consensus.matched.fasta
+ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.matched.tsv $COG_PUBLISHED_DIR/latest/majora.metadata.matched.tsv
+ln -fn -s $COG_PUBLISHED_DIR/$1/summary $COG_PUBLISHED_DIR/latest/summary
+ln -fn -s $COG_PUBLISHED_DIR/$1/ $COG_PUBLISHED_DIR/head

bin/control/cog-publish.sh

@@ -201,29 +201,7 @@ samtools faidx $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta
 
 # Repoint latest
 echo "[CPUB]" `date` " - Linking latest"
-chmod 755 $COG_PUBLISHED_DIR/$1/
-ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta $COG_PUBLISHED_DIR/elan.latest.consensus.fasta
-ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta.fai $COG_PUBLISHED_DIR/elan.latest.consensus.fasta.fai
-ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.tsv $COG_PUBLISHED_DIR/majora.latest.metadata.tsv
-ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.matched.fasta $COG_PUBLISHED_DIR/elan.latest.consensus.matched.fasta
-ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.matched.tsv $COG_PUBLISHED_DIR/majora.latest.metadata.matched.tsv
-
-# NOTE samstudio8 2021-01-28
-#      https://github.com/SamStudio8/elan-nextflow/issues/12
-#      We've now moved away from providing symlinks at a daily resolution because
-#      its hilariously expensive to maintain them and nobody actually uses them.
-#      latest/ is now a real dir rather than a symlink. To match the expected
-#      behaviour of the latest files being accessible via latest/ we'll additionally
-#      now symlink the FASTA and TSV. Eventually we can deprecate providing them
-#      above this dir.
-#      I now use a `head` symlink to keep track of the last successful run.
-ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta $COG_PUBLISHED_DIR/latest/elan.consensus.fasta
-ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.fasta.fai $COG_PUBLISHED_DIR/latest/elan.consensus.fasta.fai
-ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.tsv $COG_PUBLISHED_DIR/latest/majora.metadata.tsv
-ln -fn -s $COG_PUBLISHED_DIR/$1/elan.$1.consensus.matched.fasta $COG_PUBLISHED_DIR/latest/elan.consensus.matched.fasta
-ln -fn -s $COG_PUBLISHED_DIR/$1/majora.$1.metadata.matched.tsv $COG_PUBLISHED_DIR/latest/majora.metadata.matched.tsv
-ln -fn -s $COG_PUBLISHED_DIR/$1/summary $COG_PUBLISHED_DIR/latest/summary
-ln -fn -s $COG_PUBLISHED_DIR/$1/ $COG_PUBLISHED_DIR/head
+bash $ELAN_SOFTWARE_DIR/bin/control/cog-publish-link.sh $1
 
 # Init phylo directory
 mkdir -p $COG_RESULTS_DIR/phylogenetics/$1