Changeset 413

Timestamp:

06/23/10 23:16:39 (20 months ago)

Author:

AlexanderPico

Message:

added release variable

Location:

trunk/dbbuilder/src/org/bridgedb/download

Files:

• bacteria_download.sh (modified) (4 diffs)
• plants_download.sh (modified) (4 diffs)

trunk/dbbuilder/src/org/bridgedb/download/bacteria_download.sh

@@ -1 +1 @@
 ##!!!!!!!!!!!
-# Update "release-#" below
+# Update release-#
 ##!!!!!!!!!!!
+
+release='5'
 
 ftp_site=ftp.ensemblgenomes.org
@@ -19 +21 @@
  fi
 
-  export species_name="$species_name"; var=`echo "ls -l /pub/bacteria/release-4/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_core"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_db_name=$1
+  export species_name="$species_name"; var=`echo "ls -l /pub/bacteria/release-${release}/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_core"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_db_name=$1
 
   # check variable before proceeding
@@ -33 +35 @@
 
   # get raw tables from ftp site
-  ncftpget ${ftp_site} ./${mysql_db_name} /pub/bacteria/release-4/mysql/${mysql_db_name}/*.txt.gz
+  ncftpget ${ftp_site} ./${mysql_db_name} /pub/bacteria/release-${release}/mysql/${mysql_db_name}/*.txt.gz
   for q in ./${mysql_db_name}/*.txt.gz
   do
@@ -39 +41 @@
   done
 
-  ncftpget ${ftp_site} ./ /pub/bacteria/release-4/mysql/${mysql_db_name}/${mysql_db_name}.sql.gz
+  ncftpget ${ftp_site} ./ /pub/bacteria/release-${release}/mysql/${mysql_db_name}/${mysql_db_name}.sql.gz
   gunzip ./${mysql_db_name}.sql.gz
 

trunk/dbbuilder/src/org/bridgedb/download/plants_download.sh

@@ -1 +1 @@
 ##!!!!!!!!!!!
-# Update "release-#" below
+# Update release-#
 ##!!!!!!!!!!!
+
+release='5'
 
 ftp_site=ftp.ensemblgenomes.org
@@ -19 +21 @@
  fi
 
-  export species_name="$species_name"; var=`echo "ls -l /pub/plants/release-4/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_core"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_db_name=$1
+  export species_name="$species_name"; var=`echo "ls -l /pub/plants/release-${release}/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_core"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_db_name=$1
 
   # check variable before proceeding
@@ -31 +33 @@
   mkdir ./${mysql_db_name}
 
-
   # get raw tables from ftp site
-  ncftpget ${ftp_site} ./${mysql_db_name} /pub/plants/release-4/mysql/${mysql_db_name}/*.txt.gz
+  ncftpget ${ftp_site} ./${mysql_db_name} /pub/plants/release-${release}/mysql/${mysql_db_name}/*.txt.gz
   for q in ./${mysql_db_name}/*.txt.gz
   do
@@ -39 +40 @@
   done
 
-  ncftpget ${ftp_site} ./ /pub/plants/release-4/mysql/${mysql_db_name}/${mysql_db_name}.sql.gz
+  ncftpget ${ftp_site} ./ /pub/plants/release-${release}/mysql/${mysql_db_name}/${mysql_db_name}.sql.gz
   gunzip ./${mysql_db_name}.sql.gz