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commit/galaxy-central: greg: Better handling for mercurial command line pushes to tool shed repositories when invalid credentials are sent.
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bd6f6d645762/ Changeset: bd6f6d645762 User: greg Date: 2013-04-04 17:59:18 Summary: Better handling for mercurial command line pushes to tool shed repositories when invalid credentials are sent. Affected #: 1 file diff -r c7bd5efd3e3140a1ad0de22bf3a02e4ef8e4a948 -r bd6f6d6457624d8c59f7d821b6a478e81d70b558 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -112,6 +112,7 @@ return self.__authenticate( username, password ) def __authenticate( self, username, password ): + db_password = None # Instantiate a database connection engine = sqlalchemy.create_engine( self.db_url ) connection = engine.connect() @@ -121,14 +122,17 @@ db_email = row[ 'email' ] db_password = row[ 'password' ] connection.close() - # Check if password matches db_password when hashed. - return new_secure_hash( text_type=password ) == db_password + if db_password: + # Check if password matches db_password when hashed. + return new_secure_hash( text_type=password ) == db_password + return False def __authenticate_remote_user( self, environ, username, password ): """ Look after a remote user and "authenticate" - upstream server should already have achieved this for us, but we check that the user exists at least. Hg allow_push = must include username - some versions of mercurial blow up with 500 errors. """ + db_username = None ru_email = environ[ 'HTTP_REMOTE_USER' ].lower() ## Instantiate a database connection... engine = sqlalchemy.create_engine( self.db_url ) @@ -140,9 +144,8 @@ db_password = row[ 'password' ] db_username = row[ 'username' ] connection.close() - - """ - We could check the password here except that the function galaxy.web.framework.get_or_create_remote_user() does some random generation of - a password - so that no-one knows the password and only the hash is stored... - """ - return db_username == username + if db_username: + # We could check the password here except that the function galaxy.web.framework.get_or_create_remote_user() does some random generation of + # a password - so that no-one knows the password and only the hash is stored... + return db_username == username + return False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fixes for commit 4317a15.
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c7bd5efd3e31/ Changeset: c7bd5efd3e31 User: jgoecks Date: 2013-04-04 17:39:32 Summary: Fixes for commit 4317a15. Affected #: 1 file diff -r aad18e2fd35d0d323b8fe01d321dbb8a65bcc740 -r c7bd5efd3e3140a1ad0de22bf3a02e4ef8e4a948 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -981,15 +981,24 @@ if op == 0: # Match # Transform Ms to =s and Xs. new_op = [] - while read_pos < op_len: + total_count = 0 + while total_count < op_len and ref_seq_pos < len( ref_seq ): match, count = counter( read_seq, read_pos, ref_seq, ref_seq_pos ) + # Use min because count cannot exceed remainder of operation. + count = min( count, op_len - total_count ) if match: new_op = 7 else: new_op = 8 + new_cigar.append( ( new_op, count ) ) + total_count += count read_pos += count ref_seq_pos += count - new_cigar.append( ( new_op, count ) ) + + # If part of read falls outside of ref_seq dat, then leave + # part as M. + if total_count < op_len: + new_cigar.append( ( 0, op_len - total_count ) ) elif op == 1: # Insertion new_cigar.append( op_tuple ) elif op in [ 2, 3, 5, 6 ]: # Deletion, Skip, Soft Clipping or Padding Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fixes logout with remote_user=True (almost, logout.mako still uses the wrong template -- bug introduced in 56de0ee7932f)
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aad18e2fd35d/ Changeset: aad18e2fd35d User: dannon Date: 2013-04-04 16:19:17 Summary: Fixes logout with remote_user=True (almost, logout.mako still uses the wrong template -- bug introduced in 56de0ee7932f) Affected #: 1 file diff -r 4317a158fe8c90b01155e2a6e98f2c9ec44b29b1 -r aad18e2fd35d0d323b8fe01d321dbb8a65bcc740 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -157,10 +157,7 @@ else: menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout' ) - else: - logout_url = h.url_for( controller='/user', action='logout' ) + logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: SAM/BAM data providers: add support for modifying CIGAR string so that CIGAR can be used, along with reference sequence, to infer read sequence. Parameter clean up as well.
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4317a158fe8c/ Changeset: 4317a158fe8c User: jgoecks Date: 2013-04-04 16:16:53 Summary: SAM/BAM data providers: add support for modifying CIGAR string so that CIGAR can be used, along with reference sequence, to infer read sequence. Parameter clean up as well. Affected #: 4 files diff -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 -r 4317a158fe8c90b01155e2a6e98f2c9ec44b29b1 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -2,7 +2,7 @@ Data providers for genome visualizations. """ -import os, sys +import os, sys, operator from math import ceil, log import pkg_resources pkg_resources.require( "bx-python" ) @@ -179,7 +179,7 @@ """ start, end = int( low ), int( high ) iterator = self.get_iterator( chrom, start, end, **kwargs ) - return self.process_data( iterator, start_val, max_vals, **kwargs ) + return self.process_data( iterator, start_val, max_vals, start=start, end=end, **kwargs ) def get_genome_data( self, chroms_info, **kwargs ): """ @@ -897,7 +897,7 @@ return None return data - def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + def process_data( self, iterator, start_val=0, max_vals=None, ref_seq=None, start=0, **kwargs ): """ Returns a dict with the following attributes:: @@ -925,7 +925,86 @@ # No iterator indicates no reads. if iterator is None: return { 'data': [], 'message': None } - + + # + # Helper functions: + # + + def counter( s1, p1, s2, p2 ): + ''' + Count consecutive matches/mismatches between strings s1 and s2 + starting at p1 and p2, respectively. + ''' + + # Do initial comparison to determine whether to count matches or + # mismatches. + if s1[ p1 ] == s2[ p2 ]: + cmp_fn = operator.eq + match = True + else: + cmp_fn = operator.ne + match = False + + # Increment counts to move to next characters. + count = 1 + p1 += 1 + p2 += 1 + + # Count matches/mismatches. + while p1 < len( s1 ) and p2 < len( s2 ) and cmp_fn( s1[ p1 ], s2[ p2 ] ): + count += 1 + p1 += 1 + p2 += 1 + + return match, count + + def transform_cigar( read_seq, read_start, ref_seq, cigar ): + ''' + Returns a new cigar with =s and Xs replacing Ms; M operation is + imprecise because it can denote a sequence match or mismatch. + New cigar can be used with reference to reconstruct read sequence. + ''' + + if not ref_seq: + return read_seq, cigar + + # Set up position for reference, read. + ref_seq_pos = read_start - start + read_pos = 0 + + # Create new cigar. + new_cigar = [] + for op_tuple in cigar: + op, op_len = op_tuple + + # Op is index into string 'MIDNSHP=X' + if op == 0: # Match + # Transform Ms to =s and Xs. + new_op = [] + while read_pos < op_len: + match, count = counter( read_seq, read_pos, ref_seq, ref_seq_pos ) + if match: + new_op = 7 + else: + new_op = 8 + read_pos += count + ref_seq_pos += count + new_cigar.append( ( new_op, count ) ) + elif op == 1: # Insertion + new_cigar.append( op_tuple ) + elif op in [ 2, 3, 5, 6 ]: # Deletion, Skip, Soft Clipping or Padding + ref_seq_pos += op_len + new_cigar.append( op_tuple ) + elif op == 4: # Soft clipping + read_pos += op_len + new_cigar.append( op_tuple ) + elif op in [ 7, 8 ]: # Match or mismatch + read_pos += op_len + ref_seq_pos += op_len + new_cigar.append( op_tuple ) + + return new_cigar + # Decode strand from read flag. def decode_strand( read_flag, mask ): strand_flag = ( read_flag & mask == 0 ) @@ -934,7 +1013,11 @@ else: return "-" + # # Encode reads as list of lists. + # + if ref_seq: + ref_seq = ref_seq.upper() results = [] paired_pending = {} unmapped = 0 diff -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 -r 4317a158fe8c90b01155e2a6e98f2c9ec44b29b1 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -296,7 +296,7 @@ return False - def reference( self, trans, dbkey, chrom, low, high, **kwargs ): + def reference( self, trans, dbkey, chrom, low, high ): """ Return reference data for a build. """ diff -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 -r 4317a158fe8c90b01155e2a6e98f2c9ec44b29b1 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -176,8 +176,16 @@ if max_vals is None: max_vals = data_provider.get_default_max_vals() + # Get reference sequence for region; this is used by providers for aligned reads. + ref_seq = None + if dataset.dbkey: + data_dict = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, low=low, high=high ) + if data_dict: + ref_seq = data_dict[ 'data' ] + # Get and return data from data_provider. - result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) + result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), + ref_seq=ref_seq, **kwargs ) result.update( { 'dataset_type': data_provider.dataset_type, 'extra_info': extra_info } ) return result diff -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 -r 4317a158fe8c90b01155e2a6e98f2c9ec44b29b1 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -37,7 +37,7 @@ # Return info. rval = None if reference: - rval = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high, **kwd ) + rval = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high ) else: rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Enhance the tool shed repositories API controller with a new method to return an ordered list of changeset revision hash strings that are associated with installable revisions of a repository defined by name and owner.
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3f8ae33a02a/ Changeset: f3f8ae33a02a User: greg Date: 2013-04-04 15:56:24 Summary: Enhance the tool shed repositories API controller with a new method to return an ordered list of changeset revision hash strings that are associated with installable revisions of a repository defined by name and owner. Affected #: 3 files diff -r e587038cd8cb5d29a3c664f3dedfef0f98491918 -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -31,50 +31,27 @@ """RESTful controller for interactions with repositories in the Tool Shed.""" @web.expose_api_anonymous - def index( self, trans, deleted=False, **kwd ): + def get_ordered_installable_revisions( self, trans, name, owner, **kwd ): """ - GET /api/repositories - Displays a collection (list) of repositories. + GET /api/repository/get_ordered_installable_revisions + + :param name: the name of the Repository + :param owner: the owner of the Repository + + Returns the ordered list of changeset revision hash strings that are associated with installable revisions. As in the changelog, the + list is ordered oldest to newest. """ - # Example URL: http://localhost:9009/api/repositories - repository_dicts = [] - deleted = util.string_as_bool( deleted ) + # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_c… try: - query = trans.sa_session.query( trans.app.model.Repository ) \ - .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ - .order_by( trans.app.model.Repository.table.c.name ) \ - .all() - for repository in query: - repository_dict = repository.get_api_value( view='collection', value_mapper=default_repository_value_mapper( trans, repository ) ) - repository_dict[ 'url' ] = web.url_for( controller='repositories', - action='show', - id=trans.security.encode_id( repository.id ) ) - repository_dicts.append( repository_dict ) - return repository_dicts + # Get the repository information. + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + encoded_repository_id = trans.security.encode_id( repository.id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + ordered_installable_revisions = suc.get_ordered_downloadable_changeset_revisions( repository, repo ) + return ordered_installable_revisions except Exception, e: - message = "Error in the Tool Shed repositories API in index: %s" % str( e ) - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - - @web.expose_api_anonymous - def show( self, trans, id, **kwd ): - """ - GET /api/repositories/{encoded_repository_id} - Returns information about a repository in the Tool Shed. - - :param id: the encoded id of the Repository object - """ - # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 - try: - repository = suc.get_repository_in_tool_shed( trans, id ) - repository_dict = repository.get_api_value( view='element', value_mapper=default_repository_value_mapper( trans, repository ) ) - repository_dict[ 'url' ] = web.url_for( controller='repositories', - action='show', - id=trans.security.encode_id( repository.id ) ) - return repository_dict - except Exception, e: - message = "Error in the Tool Shed repositories API in show: %s" % str( e ) + message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: %s" % str( e ) log.error( message, exc_info=True ) trans.response.status = 500 return message @@ -103,7 +80,7 @@ "url": "/api/repositories/f9cad7b01a472135", "user_id": "f9cad7b01a472135" } - - a dictionary defining the Repsoitory revision (RepositoryMetadata). For example: + - a dictionary defining the Repository revision (RepositoryMetadata). For example: { "changeset_revision": "3a08cc21466f", "downloadable": true, @@ -171,3 +148,52 @@ log.error( message, exc_info=True ) trans.response.status = 500 return message + + @web.expose_api_anonymous + def index( self, trans, deleted=False, **kwd ): + """ + GET /api/repositories + Displays a collection (list) of repositories. + """ + # Example URL: http://localhost:9009/api/repositories + repository_dicts = [] + deleted = util.string_as_bool( deleted ) + try: + query = trans.sa_session.query( trans.app.model.Repository ) \ + .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ + .order_by( trans.app.model.Repository.table.c.name ) \ + .all() + for repository in query: + repository_dict = repository.get_api_value( view='collection', value_mapper=default_repository_value_mapper( trans, repository ) ) + repository_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository.id ) ) + repository_dicts.append( repository_dict ) + return repository_dicts + except Exception, e: + message = "Error in the Tool Shed repositories API in index: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + + @web.expose_api_anonymous + def show( self, trans, id, **kwd ): + """ + GET /api/repositories/{encoded_repository_id} + Returns information about a repository in the Tool Shed. + + :param id: the encoded id of the Repository object + """ + # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 + try: + repository = suc.get_repository_in_tool_shed( trans, id ) + repository_dict = repository.get_api_value( view='element', value_mapper=default_repository_value_mapper( trans, repository ) ) + repository_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository.id ) ) + return repository_dict + except Exception, e: + message = "Error in the Tool Shed repositories API in show: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message diff -r e587038cd8cb5d29a3c664f3dedfef0f98491918 -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -79,7 +79,8 @@ webapp.mapper.resource( 'repository', 'repositories', controller='repositories', - collection={ 'get_repository_revision_install_info' : 'GET' }, + collection={ 'get_repository_revision_install_info' : 'GET', + 'get_ordered_installable_revisions' : 'GET' }, name_prefix='repository_', path_prefix='/api', parent_resources=dict( member_name='repository', collection_name='repositories' ) ) diff -r e587038cd8cb5d29a3c664f3dedfef0f98491918 -r f3f8ae33a02a8eef02c5ecb876bfbcd67060fdc7 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1121,6 +1121,7 @@ def set_prior_installation_required( repository, required_repository ): """Return True if the received required_repository must be installed before the received repository.""" + # This method is called only from Galaxy when rendering repository dependencies for an installed tool shed repository. required_repository_tup = [ required_repository.tool_shed, required_repository.name, required_repository.owner, required_repository.changeset_revision ] # Get the list of repository dependency tuples associated with the received repository where prior_installation_required is True. required_rd_tups_that_must_be_installed = repository.requires_prior_installation_of Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1014dbf6256a/ Changeset: 1014dbf6256a User: Kyle Ellrott Date: 2013-04-02 21:36:14 Summary: Adding API ID values to HDA show_params page Affected #: 1 file diff -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 -r 1014dbf6256a44f77ed1a029193fa6d1f05bac52 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -116,6 +116,7 @@ <tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr><tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr> + <tr><td>API ID:</td><td>${trans.security.encode_id(hda.id)}</td></tr> %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif https://bitbucket.org/galaxy/galaxy-central/commits/e587038cd8cb/ Changeset: e587038cd8cb User: jgoecks Date: 2013-04-04 15:22:58 Summary: Merged in kellrott/galaxy-central (pull request #148) Adding API ID values to HDA show_params page Affected #: 1 file diff -r c43fff394fd02f868d3c8c669344c0f0870fdaa9 -r e587038cd8cb5d29a3c664f3dedfef0f98491918 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -116,6 +116,7 @@ <tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr><tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr> + <tr><td>API ID:</td><td>${trans.security.encode_id(hda.id)}</td></tr> %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16e5c3e19479/ Changeset: 16e5c3e19479 User: raj76 Date: 2013-04-01 22:59:55 Summary: Changed the logic in the trinity wrapper to handle stranded/un-stranded ran-seq data. Got the wrapper working with the latest trinity package. Affected #: 1 file diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 16e5c3e1947986102b11fe050691c722ba923696 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -20,9 +20,6 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if #else: --single $inputs.input #if $inputs.input.ext == 'fa': @@ -30,15 +27,16 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if + #end if + + #if $strand.is_strand_specific == "yes": + --SS_lib_type $strand.library_type #end if - --kmer_method meryl - + --JM 100G --full_cleanup + ## CPU and butterfly options. - --CPU 4 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> @@ -49,22 +47,28 @@ <when value="paired"><param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/><param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="FR">FR</option> - <option value="RF">RF</option> - </param><param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/></when><when value="single"><param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="F">F</option> - <option value="R">R</option> - </param></when></conditional> + <conditional name="strand"> + <param name="is_strand_specific" type="select" label="Is it strand specific data?" help=""> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + <option value="F">Forward</option> + <option value="R">Reverse</option> + </param> + </when> + </conditional><conditional name="additional_params"><param name="use_additional" type="select" label="Use Additional Params?"><option value="no">No</option> @@ -79,7 +83,7 @@ </inputs><outputs><data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> - <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> + <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/></outputs><tests></tests> https://bitbucket.org/galaxy/galaxy-central/commits/663cc29efad9/ Changeset: 663cc29efad9 User: raj76 Date: 2013-04-04 07:16:09 Summary: Removed --full_cleanup as galaxy deletes the job's working directory. Changed the memory for Jellyfish to 10G from 100G. Probably better as a default value. Affected #: 1 file diff -r 16e5c3e1947986102b11fe050691c722ba923696 -r 663cc29efad9ec1a54bfc108b6be7e34a1dc6b17 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -33,7 +33,7 @@ --SS_lib_type $strand.library_type #end if - --JM 100G --full_cleanup + --JM 10G ## CPU and butterfly options. --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 @@ -83,7 +83,7 @@ </inputs><outputs><data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> - <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/> + <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/></outputs><tests></tests> https://bitbucket.org/galaxy/galaxy-central/commits/c43fff394fd0/ Changeset: c43fff394fd0 User: jgoecks Date: 2013-04-04 15:13:18 Summary: Merged in raj76/galaxy-central-tools (pull request #147) Changed the logic in the trinity wrapper to handle stranded/un-stranded ran-seq data. Got the wrapper working with the latest trinity package. Affected #: 1 file diff -r c7fae25b9fa35533afb15df6a6fdb47d677f8110 -r c43fff394fd02f868d3c8c669344c0f0870fdaa9 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -20,9 +20,6 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if #else: --single $inputs.input #if $inputs.input.ext == 'fa': @@ -30,15 +27,16 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if + #end if + + #if $strand.is_strand_specific == "yes": + --SS_lib_type $strand.library_type #end if - --kmer_method meryl - + --JM 10G + ## CPU and butterfly options. - --CPU 4 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> @@ -49,22 +47,28 @@ <when value="paired"><param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/><param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="FR">FR</option> - <option value="RF">RF</option> - </param><param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/></when><when value="single"><param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="F">F</option> - <option value="R">R</option> - </param></when></conditional> + <conditional name="strand"> + <param name="is_strand_specific" type="select" label="Is it strand specific data?" help=""> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + <option value="F">Forward</option> + <option value="R">Reverse</option> + </param> + </when> + </conditional><conditional name="additional_params"><param name="use_additional" type="select" label="Use Additional Params?"><option value="no">No</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ac5c2aca2b7/ Changeset: 7ac5c2aca2b7 User: jmchilton Date: 2013-03-24 17:36:16 Summary: For task parallelism if no shared_inputs attribute is defined just assume all variables that are not being split are being shared. I cannot think of a good reason not to do this. Affected #: 1 file diff -r f6743b36ce0a54e49acf06d09e03d01584d55514 -r 7ac5c2aca2b7024f6d1444ab46d562bb838fed6d lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -19,8 +19,10 @@ split_inputs = [x.strip() for x in split_inputs.split(",")] shared_inputs=parallel_settings.get("shared_inputs") + auto_shared_inputs = False if shared_inputs is None: shared_inputs = [] + auto_shared_inputs = True else: shared_inputs = [x.strip() for x in shared_inputs.split(",")] illegal_inputs = [x for x in shared_inputs if x in split_inputs] @@ -45,6 +47,8 @@ type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) elif input.name in shared_inputs: pass # pass original file name + elif auto_shared_inputs: + shared_inputs.append(input.name) else: log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) log.exception(log_error) https://bitbucket.org/galaxy/galaxy-central/commits/c7fae25b9fa3/ Changeset: c7fae25b9fa3 User: dannon Date: 2013-04-04 14:58:16 Summary: Merged in jmchilton/galaxy-central-library-refactoring (pull request #142) Small Task Splitting Simpliciation Affected #: 1 file diff -r b7a05dcaa5211ac29af0d3aa201a526e51eb0bfa -r c7fae25b9fa35533afb15df6a6fdb47d677f8110 lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -19,8 +19,10 @@ split_inputs = [x.strip() for x in split_inputs.split(",")] shared_inputs=parallel_settings.get("shared_inputs") + auto_shared_inputs = False if shared_inputs is None: shared_inputs = [] + auto_shared_inputs = True else: shared_inputs = [x.strip() for x in shared_inputs.split(",")] illegal_inputs = [x for x in shared_inputs if x in split_inputs] @@ -45,6 +47,8 @@ type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) elif input.name in shared_inputs: pass # pass original file name + elif auto_shared_inputs: + shared_inputs.append(input.name) else: log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) log.exception(log_error) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/62d0924f163b/ Changeset: 62d0924f163b User: nsoranzo Date: 2013-03-06 12:37:08 Summary: Fix file extension determination Extension was determined uncorrectly for filenames with more than 1 dot Affected #: 1 file diff -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 -r 62d0924f163b8731adaf582056587c0c4f415a7b tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -247,7 +247,7 @@ #binary_ok = False parts = dataset.name.split( "." ) if len( parts ) > 1: - ext = parts[1].strip().lower() + ext = parts[-1].strip().lower() if not Binary.is_ext_unsniffable(ext): file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) return https://bitbucket.org/galaxy/galaxy-central/commits/d6f866cbf12d/ Changeset: d6f866cbf12d User: nsoranzo Date: 2013-03-06 12:39:04 Summary: Add generic ASN.1 text and binary datatypes Affected #: 3 files diff -r 62d0924f163b8731adaf582056587c0c4f415a7b -r d6f866cbf12d0242089fbbbfb799fb20600441cf datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -3,6 +3,8 @@ <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"><datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /><datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/><datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/><datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> diff -r 62d0924f163b8731adaf582056587c0c4f415a7b -r d6f866cbf12d0242089fbbbfb799fb20600441cf lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -85,6 +85,12 @@ Binary.register_unsniffable_binary_ext("ab1") +class GenericAsn1Binary( Binary ): + """Class for generic ASN.1 binary format""" + file_ext = "asn1-binary" + +Binary.register_unsniffable_binary_ext("asn1-binary") + class Bam( Binary ): """Class describing a BAM binary file""" file_ext = "bam" diff -r 62d0924f163b8731adaf582056587c0c4f415a7b -r d6f866cbf12d0242089fbbbfb799fb20600441cf lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -739,6 +739,10 @@ f.close() split = classmethod(split) +class GenericAsn1( Text ): + """Class for generic ASN.1 text format""" + file_ext = 'asn1' + class LineCount( Text ): """ Dataset contains a single line with a single integer that denotes the https://bitbucket.org/galaxy/galaxy-central/commits/b7a05dcaa521/ Changeset: b7a05dcaa521 User: dannon Date: 2013-04-04 14:41:54 Summary: Merged in nsoranzo/galaxy-central (pull request #135) Add generic ASN.1 text and binary datatypes Affected #: 4 files diff -r 740d8a84d0abeaf28c423fe98b8bee121ba92934 -r b7a05dcaa5211ac29af0d3aa201a526e51eb0bfa datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -3,6 +3,8 @@ <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"><datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/> + <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /> + <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /><datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/><datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/><datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> diff -r 740d8a84d0abeaf28c423fe98b8bee121ba92934 -r b7a05dcaa5211ac29af0d3aa201a526e51eb0bfa lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -85,6 +85,12 @@ Binary.register_unsniffable_binary_ext("ab1") +class GenericAsn1Binary( Binary ): + """Class for generic ASN.1 binary format""" + file_ext = "asn1-binary" + +Binary.register_unsniffable_binary_ext("asn1-binary") + class Bam( Binary ): """Class describing a BAM binary file""" file_ext = "bam" diff -r 740d8a84d0abeaf28c423fe98b8bee121ba92934 -r b7a05dcaa5211ac29af0d3aa201a526e51eb0bfa lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -739,6 +739,10 @@ f.close() split = classmethod(split) +class GenericAsn1( Text ): + """Class for generic ASN.1 text format""" + file_ext = 'asn1' + class LineCount( Text ): """ Dataset contains a single line with a single integer that denotes the diff -r 740d8a84d0abeaf28c423fe98b8bee121ba92934 -r b7a05dcaa5211ac29af0d3aa201a526e51eb0bfa tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -247,7 +247,7 @@ #binary_ok = False parts = dataset.name.split( "." ) if len( parts ) > 1: - ext = parts[1].strip().lower() + ext = parts[-1].strip().lower() if not Binary.is_ext_unsniffable(ext): file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) return Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Apr '13

04 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6c234a64e7b2/ Changeset: 6c234a64e7b2 Branch: stable User: natefoo Date: 2013-04-04 14:20:46 Summary: Fix bug in the sample advanced job configuration noticed by Anthonius deBoer. Affected #: 1 file diff -r da2d6ee29f309454f35d9f8cf9d6eb837c87a7dd -r 6c234a64e7b287565c968f128b047aabec78ec50 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -6,7 +6,7 @@ --><plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> - <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/><plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> https://bitbucket.org/galaxy/galaxy-central/commits/740d8a84d0ab/ Changeset: 740d8a84d0ab User: natefoo Date: 2013-04-04 14:21:09 Summary: Merge stable. Affected #: 1 file diff -r 7de5ccb2b253d24dc3d9cc5b681ee3662d57d565 -r 740d8a84d0abeaf28c423fe98b8bee121ba92934 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -6,7 +6,7 @@ --><plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> - <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> + <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/><plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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