Commit a5e56398 authored by Andy Yates's avatar Andy Yates
Browse files

Module locations not updated

parent b22804ef
......@@ -71,7 +71,7 @@ sub pipeline_analyses {
{
-logic_name => 'ScheduleSpecies',
-module => 'FASTADumper::ReuseSpeciesFactory',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::ReuseSpeciesFactory',
-parameters => {
species => $self->o('species'),
sequence_type_list => $self->o('dump_types'),
......@@ -93,7 +93,7 @@ sub pipeline_analyses {
{
-logic_name => 'DumpDNA',
-module => 'FASTADumper::DumpFile',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::DumpFile',
-can_be_empty => 1,
-flow_into => {
1 => 'ConcatFiles'
......@@ -106,7 +106,7 @@ sub pipeline_analyses {
{
-logic_name => 'DumpGenes',
-module => 'FASTADumper::DumpFile',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::DumpFile',
-flow_into => {
2 => ['BlastPepIndex'],
3 => ['BlastGeneIndex']
......@@ -120,7 +120,7 @@ sub pipeline_analyses {
{
-logic_name => 'ConcatFiles',
-module => 'FASTADumper::ConcatFiles',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::ConcatFiles',
-rc_id => 1,
-can_be_empty => 1,
-flow_into => {
......@@ -132,7 +132,7 @@ sub pipeline_analyses {
{
-logic_name => 'CopyDNA',
-module => 'FASTADumper::CopyDNA',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::CopyDNA',
-rc_id => 1,
-can_be_empty => 1,
-hive_capacity => 5,
......@@ -146,7 +146,7 @@ sub pipeline_analyses {
{
-logic_name => 'BlastDNAIndex',
-module => 'FASTADumper::WuBlastIndexer',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::WuBlastIndexer',
-parameters => {
molecule => 'dna', type => 'genomic', program => $self->o('wublast_exe')
},
......@@ -157,7 +157,7 @@ sub pipeline_analyses {
{
-logic_name => 'BlastPepIndex',
-module => 'FASTADumper::WuBlastIndexer',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::WuBlastIndexer',
-parameters => {
molecule => 'pep', type => 'genes', program => $self->o('wublast_exe')
},
......@@ -171,7 +171,7 @@ sub pipeline_analyses {
{
-logic_name => 'BlastGeneIndex',
-module => 'FASTADumper::BlastIndexer',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::BlastIndexer',
-parameters => {
molecule => 'dna', type => 'genes', program => $self->o('wublast_exe')
},
......@@ -185,7 +185,7 @@ sub pipeline_analyses {
{
-logic_name => 'BlatDNAIndex',
-module => 'FASTADumper::BlatIndexer',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::BlatIndexer',
-parameters => {
port_offset => $self->o('port_offset'),
program => $self->o('blat_exe'),
......@@ -199,7 +199,7 @@ sub pipeline_analyses {
######## COPYING
{
-logic_name => 'SCPBlast',
-module => 'FASTADumper::SCPBlast',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::SCPBlast',
-parameters => {
target_servers => $self->o('blast_servers'),
genomic_dir => $self->o('blast_genomic_dir'),
......@@ -219,7 +219,7 @@ sub pipeline_analyses {
{
-logic_name => 'ChecksumGeneratorFactory',
-module => 'FASTADumper::FindDirs',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::FindDirs',
-parameters => {
column_names => [qw/dir/],
input_id => { 'dir' => '#dir#' },
......@@ -232,7 +232,7 @@ sub pipeline_analyses {
{
-logic_name => 'ChecksumGenerator',
-module => 'FASTADumper::ChecksumGenerator',
-module => 'Bio::EnsEMBL::Pipeline::FASTA::ChecksumGenerator',
-hive_capacity => 10,
-rc_id => 1,
},
......
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