Add shell script for autoupdate seqrepo

misc/update_seqrepo.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+SEQREPO_RELEASE_DIR=/biocommons/dl.biocommons.org/seqrepo
+SEQREPO_ROOT=/usr/local/share/seqrepo
+
+mkdir -p $SEQREPO_ROOT
+rm -rf $SEQREPO_ROOT/master
+
+
+# Copy the latest release to work on
+LATEST_RELEASE=$(ls -d $SEQREPO_RELEASE_DIR/????-??-?? | tail -n 1)
+
+cp -a $LATEST_RELEASE $SEQREPO_ROOT/master
+
+
+# Add write permission to folders and databases
+chmod u+w $SEQREPO_ROOT/master $SEQREPO_ROOT/master/sequences \
+          $SEQREPO_ROOT/master/aliases.sqlite3 $SEQREPO_ROOT/master/sequences/db.sqlite3
+
+chmod u+w $(ls -d $SEQREPO_ROOT/master/sequences/*/ | tail -n 1)
+
+
+# Load sequences
+seqrepo -r $SEQREPO_ROOT load -n NCBI \
+    /biocommons/mirrors-ncbi/latest/refseq/H_sapiens/mRNA_Prot/human.*f[na]a.gz \
+    /biocommons/mirrors-ncbi/latest/refseq/H_sapiens/RefSeqGene/refseqgene.*f[na]a.gz \
+    /biocommons/mirrors-ncbi/latest/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/*/GCF_*_genomic.f[na]a.gz
+
+if [ $? -ne 0 ]; then
+    echo "Error: seqrepo load failed"
+    exit 1
+fi
+
+
+# Make a snapshot
+seqrepo -r $SEQREPO_ROOT -v snapshot
+
+if [ $? -ne 0 ]; then
+    echo "Error: seqrepo snapshot failed"
+    exit 2
+fi
+
+
+# Push snapshot to download area
+NEW_RELEASE=$(ls -d $SEQREPO_ROOT/????-??-?? | tail -n 1 | rev | cut -f1 -d'/' | rev)
+
+rsync -aP --link-dest=$LATEST_RELEASE/ $SEQREPO_ROOT/$NEW_RELEASE/ $SEQREPO_RELEASE_DIR/$NEW_RELEASE/
+