Merge pull request #10 from sanger-pathogens/update-to-scratch125

change to /data

README.md

@@ -63,7 +63,7 @@ Add references to the pipelines.
 Options: -o       overwrite index files [False]
          -p INT   number of processors [1]
          -r STR   reference store directory [/nfs/pathogen/refs]
-         -d STR   production references direcotry [/lustre/scratch118/.../refs]
+         -d STR   production references direcotry [/data/pam.../refs]
          -m STR   reference metadata filename [metadata.json]
          -n       use a hash of the file as the reference name [FALSE]
          -i STR   toplevel index filename [refs.index]
@@ -80,4 +80,4 @@ Advanced options:
 Bio-ReferenceManager is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/Bio-ReferenceManager/blob/master/GPL-LICENSE).
 
 ## Feedback/Issues
-Please report any issues to the [issues page](https://github.com/sanger-pathogens/Bio-ReferenceManager/issues) or email [email protected].
+Please report any issues to the [issues page](https://github.com/sanger-pathogens/Bio-ReferenceManager/issues) or email [email protected].

lib/Bio/ReferenceManager/CommandLine/NCBIDownload.pm

@@ -25,7 +25,7 @@ has 'downloaded_filename'            => ( is => 'rw', isa => 'Str',  default =>
 has 'output_directory'               => ( is => 'rw', isa => 'Str',  default => 'downloaded_assemblies' );
 has 'download_only_new'              => ( is => 'rw', isa => 'Bool', default => 1 );
 has 'dont_redownload_assembly_stats' => ( is => 'rw', isa => 'Bool', default => 0 );
-has 'index_filename'  => ( is => 'rw', isa => 'Str', default => '/lustre/scratch118/infgen/pathogen/pathpipe/refs/refs.index' );
+has 'index_filename'  => ( is => 'rw', isa => 'Str', default => '/data/pam/applications/vr-pipelines/refs/refs.index' );
 has 'assembly_type'   => ( is => 'rw', isa => 'Str', default => "Complete Genome" );
 has 'assembly_latest' => ( is => 'rw', isa => 'Str', default => "latest" );
 has 'processors'      => ( is => 'rw', isa => 'Int', default => 1 );
@@ -110,7 +110,7 @@ By default it will download all new complete genomes from RefSeq
 
 Options: 
   -u STR NCBI assembly stats table [ftp://ftp.ncbi.nlm.nih.gov/.../assembly_summary.txt]
-  -i STR Top level refs index filename [/lustre/scratch118/.../refs.index]
+  -i STR Top level refs index filename [/data/pam.../refs.index]
   -e     Download all genomes, not just new ones [FALSE]
   -p INT number of processors [1]
   -o STR output directory [downloaded_assemblies]

lib/Bio/ReferenceManager/CommandLine/RefMan.pm

@@ -23,7 +23,7 @@ has 'verbose'     => ( is => 'rw', isa => 'Bool',     default  => 0 );
 has 'input_files' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] } );
 has 'reference_store_dir'      => ( is => 'rw', isa => 'Str', default => '/nfs/pathogen/refs' );
 has 'reference_metadata'       => ( is => 'rw', isa => 'Str', default => 'metadata.json' );
-has 'production_reference_dir' => ( is => 'rw', isa => 'Str', default => '/lustre/scratch118/infgen/pathogen/pathpipe/refs' );
+has 'production_reference_dir' => ( is => 'rw', isa => 'Str', default => '/data/pam/applications/vr-pipelines/refs' );
 has 'processors'               => ( is => 'rw', isa => 'Int', default => 1 );
 
 # for PrepareFasta
@@ -134,7 +134,7 @@ Add references to the pipelines.
 Options: -o       overwrite index files [False]
          -p INT   number of processors [1]
          -r STR   reference store directory [/nfs/pathogen/refs]
-         -d STR   production references direcotry [/lustre/scratch118/.../refs]
+         -d STR   production references direcotry [/data/pam.../refs]
          -m STR   reference metadata filename [metadata.json]
          -n       use a hash of the file as the reference name [FALSE]
          -i STR   toplevel index filename [refs.index]