From 401221c067421bc351a30f3de3e435ea0f557af7 Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Thu, 26 Aug 2021 21:46:31 +0000 Subject: [PATCH] removing (for now) the processing skipping options --- single_species_build.sh | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/single_species_build.sh b/single_species_build.sh index 9351ee8..e4567a7 100755 --- a/single_species_build.sh +++ b/single_species_build.sh @@ -52,14 +52,14 @@ then fi fi -if [ -z "$UPDATE_ONLY" ] -then - SKIPFLATFILE=" --skipflatfile " - ONLYTRACKLIST=" --onlytracklist " -else - SLIPFLATFILE=" " - ONLYTRACKLIST=" " -fi +#if [ -z "$UPDATE_ONLY" ] +#then +# SKIPFLATFILE=" --skipflatfile " +# ONLYTRACKLIST=" --onlytracklist " +#else +# SLIPFLATFILE=" " +# ONLYTRACKLIST=" " +#fi MAKEPATH=/website-genome-browsers/jbrowse/bin/make_jbrowse.pl @@ -69,7 +69,8 @@ LOGFILE=$SPECIES LOGFILE+=".log" #this is by far the longest running portion of the script (typically a few hours) -$MAKEPATH $SKIPFLATFILE --conf $CONFPATH --quiet --species $SPECIES 2>1 | grep -v "Deep recursion"; mv 1 $LOGFILE +#$MAKEPATH $SKIPFLATFILE --conf $CONFPATH --quiet --species $SPECIES 2>1 | grep -v "Deep recursion"; mv 1 $LOGFILE +$MAKEPATH --conf $CONFPATH --quiet --species $SPECIES 2>1 | grep -v "Deep recursion"; mv 1 $LOGFILE INLINEINCLUDEPATH=/website-genome-browsers/jbrowse/bin/inline_includes.pl @@ -87,7 +88,8 @@ UPLOADTOS3PATH=/agr_jbrowse_config/scripts/upload_to_S3.pl REMOTEPATH="MOD-jbrowses/WormBase/WS$RELEASE/$SPECIES" #REMOTEPATH="test/WS$RELEASE/$SPECIES" -$UPLOADTOS3PATH $ONLYTRACKLIST --bucket $AWSBUCKET --local "$SPECIES/" --remote $REMOTEPATH --AWSACCESS $AWSACCESS --AWSSECRET $AWSSECRET +#$UPLOADTOS3PATH $ONLYTRACKLIST --bucket $AWSBUCKET --local "$SPECIES/" --remote $REMOTEPATH --AWSACCESS $AWSACCESS --AWSSECRET $AWSSECRET +$UPLOADTOS3PATH --bucket $AWSBUCKET --local "$SPECIES/" --remote $REMOTEPATH --AWSACCESS $AWSACCESS --AWSSECRET $AWSSECRET