November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 2c934a168af9: More tweaking of lines_diff for cuffdiff test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288633591 14400 # Node ID 2c934a168af968dc84300412220c2f2cb74bf676 # Parent 9415f380f2e7d4aca44f74923b6984ab3bcc1dfb More tweaking of lines_diff for cuffdiff test. --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -78,11 +78,11 @@ TODO: can we find datasets that lead to deterministic behavior? --><output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> - <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="8"/> - <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="4"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="8"/><output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/><output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/><output name="splicing_diff" file="cuffdiff_out9.txt"/>

1 0

galaxy-dist commit 9415f380f2e7: Added validation checks in the data transfer script for sample tracking
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288380270 14400 # Node ID 9415f380f2e7d4aca44f74923b6984ab3bcc1dfb # Parent 0518ce52d8d3ca15ec6070f2addb4bfe7608c23b Added validation checks in the data transfer script for sample tracking --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -3,12 +3,12 @@ Data Transfer Script: Sequencer to Galaxy -This script is called from Galaxy LIMS once the lab admin starts the data -transfer process using the user interface. +This script is called from Galaxy RabbitMQ listener ( amqp_consumer.py ) once +the lab admin starts the data transfer process using the user interface. Usage: -python data_transfer.py <data_transfer_xml><config_id_secret> +python data_transfer.py <config_file> """ @@ -19,13 +19,13 @@ import urllib,urllib2, cookielib, shutil import logging, time, datetime import xml.dom.minidom -log = logging.getLogger("datatx_"+str(os.getpid())) -log.setLevel(logging.DEBUG) -fh = logging.FileHandler("data_transfer.log") -fh.setLevel(logging.DEBUG) -formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") -fh.setFormatter(formatter) -log.addHandler(fh) +log = logging.getLogger( "datatx_" + str( os.getpid() ) ) +log.setLevel( logging.DEBUG ) +fh = logging.FileHandler( "data_transfer.log" ) +fh.setLevel( logging.DEBUG ) +formatter = logging.Formatter( "%(asctime)s - %(name)s - %(message)s" ) +fh.setFormatter( formatter ) +log.addHandler( fh ) api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] sys.path.extend( api_path ) @@ -47,60 +47,76 @@ import pexpect pkg_resources.require( "simplejson" ) import simplejson -class DataTransfer(object): - - def __init__(self, msg, config_file): - log.info(msg) - self.dom = xml.dom.minidom.parseString(msg) - self.sequencer_host = self.get_value(self.dom, 'data_host') - self.sequencer_username = self.get_value(self.dom, 'data_user') - self.sequencer_password = self.get_value(self.dom, 'data_password') - self.request_id = self.get_value(self.dom, 'request_id') - self.sample_id = self.get_value(self.dom, 'sample_id') - self.library_id = self.get_value(self.dom, 'library_id') - self.folder_id = self.get_value(self.dom, 'folder_id') +class DataTransfer( object ): + + def __init__( self, msg, config_file ): + log.info( msg ) + self.dom = xml.dom.minidom.parseString( msg ) + self.sequencer_host = self.get_value( self.dom, 'data_host' ) + self.sequencer_username = self.get_value( self.dom, 'data_user' ) + self.sequencer_password = self.get_value( self.dom, 'data_password' ) + self.request_id = self.get_value( self.dom, 'request_id' ) + self.sample_id = self.get_value( self.dom, 'sample_id' ) + self.library_id = self.get_value( self.dom, 'library_id' ) + self.folder_id = self.get_value( self.dom, 'folder_id' ) self.dataset_files = [] count=0 while True: - dataset_id = self.get_value_index(self.dom, 'dataset_id', count) - file = self.get_value_index(self.dom, 'file', count) - name = self.get_value_index(self.dom, 'name', count) - if file: - self.dataset_files.append(dict(name=name, - dataset_id=int(dataset_id), - file=file)) - else: - break - count=count+1 + dataset_id = self.get_value_index( self.dom, 'dataset_id', count ) + file = self.get_value_index( self.dom, 'file', count ) + name = self.get_value_index( self.dom, 'name', count ) + if file: + self.dataset_files.append( dict( name=name, + dataset_id=int( dataset_id ), + file=file ) ) + else: + break + count=count+1 try: # Retrieve the upload user login information from the config file - transfer_datasets_config = ConfigParser.ConfigParser() - transfer_datasets_config.read('transfer_datasets.ini') - self.data_transfer_user_email = transfer_datasets_config.get("data_transfer_user_login_info", "email") - self.data_transfer_user_password = transfer_datasets_config.get("data_transfer_user_login_info", "password") - self.api_key = transfer_datasets_config.get("data_transfer_user_login_info", "api_key") - self.http_server_section = transfer_datasets_config.get("universe_wsgi_config", "http_server_section") - config = ConfigParser.ConfigParser() - config.read( config_file ) - self.server_host = config.get(self.http_server_section, "host") - self.server_port = config.get(self.http_server_section, "port") - self.database_connection = config.get("app:main", "database_connection") - self.import_dir = config.get("app:main", "library_import_dir") - self.config_id_secret = config.get("app:main", "id_secret") - - # create the destination directory within the import directory - self.server_dir = os.path.join( self.import_dir, 'datatx_'+str(os.getpid())+'_'+datetime.date.today().strftime("%d%b%Y") ) - os.mkdir(self.server_dir) - if not os.path.exists(self.server_dir): - raise Exception + transfer_datasets_config = ConfigParser.ConfigParser( ) + transfer_datasets_config.read( 'transfer_datasets.ini' ) + self.data_transfer_user_email = transfer_datasets_config.get( "data_transfer_user_login_info", "email" ) + self.data_transfer_user_password = transfer_datasets_config.get( "data_transfer_user_login_info", "password" ) + self.api_key = transfer_datasets_config.get( "data_transfer_user_login_info", "api_key" ) + self.http_server_section = transfer_datasets_config.get( "universe_wsgi_config", "http_server_section" ) except: - log.error(traceback.format_exc()) - log.error('FATAL ERROR') - if self.database_connection: - self.error_and_exit('Error') + log.error( traceback.format_exc() ) + log.error( 'ERROR reading config values from transfer_datasets.ini.' ) sys.exit(1) + # read config variables + config = ConfigParser.ConfigParser() + retval = config.read( config_file ) + if not retval: + error_msg = 'FATAL ERROR: Unable to open config file %s.' % config_file + log.error( error_msg ) + sys.exit(1) + try: + self.server_host = config.get( self.http_server_section, "host" ) + except ConfigParser.NoOptionError,e: + self.server_host = '127.0.0.1' + try: + self.server_port = config.get( self.http_server_section, "port" ) + except ConfigParser.NoOptionError,e: + self.server_port = '8080' + try: + self.config_id_secret = config.get( "app:main", "id_secret" ) + except ConfigParser.NoOptionError,e: + self.config_id_secret = "USING THE DEFAULT IS NOT SECURE!" + try: + self.import_dir = config.get( "app:main", "library_import_dir" ) + except ConfigParser.NoOptionError,e: + log.error( 'ERROR: library_import_dir config variable is not set in %s. ' % config_file ) + sys.exit( 1 ) + # create the destination directory within the import directory + self.server_dir = os.path.join( self.import_dir, + 'datatx_' + str( os.getpid() ) + '_' + datetime.date.today( ).strftime( "%d%b%Y" ) ) + try: + os.mkdir( self.server_dir ) + except Exception, e: + self.error_and_exit( str( e ) ) - def start(self): + def start( self ): ''' This method executes the file transfer from the sequencer, adds the dataset to the data library & finally updates the data transfer status in the db @@ -110,72 +126,73 @@ class DataTransfer(object): # add the dataset to the given library self.add_to_library() # update the data transfer status in the db - self.update_status(SampleDataset.transfer_status.COMPLETE) + self.update_status( SampleDataset.transfer_status.COMPLETE ) # cleanup #self.cleanup() - sys.exit(0) + sys.exit( 0 ) - def cleanup(self): + def cleanup( self ): ''' remove the directory created to store the dataset files temporarily before adding the same to the data library ''' try: - time.sleep(60) + time.sleep( 60 ) shutil.rmtree( self.server_dir ) except: self.error_and_exit() - def error_and_exit(self, msg=''): + def error_and_exit( self, msg='' ): ''' This method is called any exception is raised. This prints the traceback and terminates this script ''' - log.error(traceback.format_exc()) - log.error('FATAL ERROR.'+msg) - self.update_status('Error', 'All', msg+"\n"+traceback.format_exc()) - sys.exit(1) + log.error( traceback.format_exc() ) + log.error( 'FATAL ERROR.' + msg ) + self.update_status( 'Error', 'All', msg ) + sys.exit( 1 ) - def transfer_files(self): + def transfer_files( self ): ''' This method executes a scp process using pexpect library to transfer the dataset file from the remote sequencer to the Galaxy server ''' - def print_ticks(d): + def print_ticks( d ): pass - for i, df in enumerate(self.dataset_files): - self.update_status(SampleDataset.transfer_status.TRANSFERRING, df['dataset_id']) + for i, dataset_file in enumerate( self.dataset_files ): + self.update_status( SampleDataset.transfer_status.TRANSFERRING, dataset_file[ 'dataset_id' ] ) try: cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.sequencer_username, self.sequencer_host, - df['file'].replace(' ', '\ '), - self.server_dir.replace(' ', '\ '), - df['name'].replace(' ', '\ ') ) - log.debug(cmd) - output = pexpect.run(cmd, events={'.ssword:*': self.sequencer_password+'\r\n', - pexpect.TIMEOUT:print_ticks}, - timeout=10) - log.debug(output) - path = os.path.join(self.server_dir, os.path.basename(df['name'])) - if not os.path.exists(path): - msg = 'Could not find the local file after transfer (%s)' % path - log.error(msg) - raise Exception(msg) + dataset_file[ 'file' ].replace( ' ', '\ ' ), + self.server_dir.replace( ' ', '\ ' ), + dataset_file[ 'name' ].replace( ' ', '\ ' ) ) + log.debug( cmd ) + output = pexpect.run( cmd, + events={ '.ssword:*': self.sequencer_password+'\r\n', + pexpect.TIMEOUT: print_ticks }, + timeout=10 ) + log.debug( output ) + path = os.path.join( self.server_dir, os.path.basename( dataset_file[ 'name' ] ) ) + if not os.path.exists( path ): + msg = 'Could not find the local file after transfer ( %s ).' % path + log.error( msg ) + raise Exception( msg ) except Exception, e: msg = traceback.format_exc() - self.update_status('Error', df['dataset_id'], msg) + self.update_status( 'Error', dataset_file['dataset_id'], msg) - def add_to_library(self): + def add_to_library( self ): ''' This method adds the dataset file to the target data library & folder by opening the corresponding url in Galaxy server running. ''' - self.update_status(SampleDataset.transfer_status.ADD_TO_LIBRARY) + self.update_status( SampleDataset.transfer_status.ADD_TO_LIBRARY ) try: data = {} - data[ 'folder_id' ] = api.encode_id( self.config_id_secret, '%s.%s' % ( 'folder', self.folder_id ) ) + data[ 'folder_id' ] = api.encode_id( self.config_id_secret, '%s.%s' % ( 'folder', self.folder_id ) ) data[ 'file_type' ] = 'auto' data[ 'server_dir' ] = self.server_dir data[ 'dbkey' ] = '' @@ -183,23 +200,23 @@ class DataTransfer(object): data[ 'create_type' ] = 'file' url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, self.server_port, - api.encode_id( self.config_id_secret, self.library_id ) ) - log.debug( str( ( self.api_key, url, data ) ) ) + api.encode_id( self.config_id_secret, self.library_id ) ) + log.debug( str( ( self.api_key, url, data ) ) ) retval = api.submit( self.api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) + log.debug( str( retval ) ) except Exception, e: - self.error_and_exit( str( e ) ) + self.error_and_exit( str( e ) ) - def update_status(self, status, dataset_id='All', msg=''): + def update_status( self, status, dataset_id='All', msg='' ): ''' Update the data transfer status for this dataset in the database ''' try: - log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_id), str(self.sample_id) ) ) + log.debug( 'Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str( dataset_id ), str( self.sample_id) ) ) sample_dataset_ids = [] if dataset_id == 'All': for dataset in self.dataset_files: - sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset['dataset_id'] ) ) + sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset[ 'dataset_id' ] ) ) else: sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset_id ) ) # update the transfer status @@ -208,37 +225,37 @@ class DataTransfer(object): data[ 'sample_dataset_ids' ] = sample_dataset_ids data[ 'new_status' ] = status data[ 'error_msg' ] = msg - url = "http://%s:%s/api/requests/%s" % ( self.server_host, + url = "http://%s:%s/api/requests/%s" % ( self.server_host, self.server_port, - api.encode_id( self.config_id_secret, self.request_id ) ) - log.debug(str((self.api_key, url, data))) + api.encode_id( self.config_id_secret, self.request_id ) ) + log.debug( str( ( self.api_key, url, data))) retval = api.update( self.api_key, url, data, return_formatted=False ) log.debug( str( retval ) ) except urllib2.URLError, e: - log.debug( 'ERROR(sample_dataset_transfer_status (%s)): %s' % ( url, str(e) ) ) - log.error(traceback.format_exc()) + log.debug( 'ERROR( sample_dataset_transfer_status ( %s ) ): %s' % ( url, str( e ) ) ) + log.error( traceback.format_exc() ) except: - log.error(traceback.format_exc()) - log.error('FATAL ERROR') - sys.exit(1) + log.error( traceback.format_exc() ) + log.error( 'FATAL ERROR' ) + sys.exit( 1 ) - def get_value(self, dom, tag_name): + def get_value( self, dom, tag_name ): ''' This method extracts the tag value from the xml message ''' - nodelist = dom.getElementsByTagName(tag_name)[0].childNodes + nodelist = dom.getElementsByTagName( tag_name )[ 0 ].childNodes rc = "" for node in nodelist: if node.nodeType == node.TEXT_NODE: rc = rc + node.data return rc - def get_value_index(self, dom, tag_name, dataset_id): + def get_value_index( self, dom, tag_name, dataset_id ): ''' This method extracts the tag value from the xml message ''' try: - nodelist = dom.getElementsByTagName(tag_name)[dataset_id].childNodes + nodelist = dom.getElementsByTagName( tag_name )[ dataset_id ].childNodes except: return None rc = "" @@ -248,11 +265,11 @@ class DataTransfer(object): return rc if __name__ == '__main__': - log.info('STARTING %i %s' % (os.getpid(), str(sys.argv))) + log.info( 'STARTING %i %s' % ( os.getpid(), str( sys.argv ) ) ) # # Start the daemon # - dt = DataTransfer(sys.argv[1], sys.argv[2]) + dt = DataTransfer( sys.argv[1], sys.argv[2]) dt.start() - sys.exit(0) + sys.exit( 0 )

1 0

galaxy-dist commit 9c6040ab75a8: Fix for refresh_on_change javascript.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Daniel Blankenberg <dan(a)bx.psu.edu> # Date 1288196760 14400 # Node ID 9c6040ab75a8397a5708cfec4edfe216927b8220 # Parent a2e4d36c4318bc4ce73af9df869ae4071af33d55 Fix for refresh_on_change javascript. --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -290,8 +290,8 @@ function replace_big_select_inputs(min_l var try_refresh_fn = function() { // Get new value and see if it can be matched. var new_value = select_mapping[text_input_elt.attr('value')]; - if (new_value !== null && new_value !== undefined) { - if ($.inArray(new_value, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + if (last_selected_value !== new_value && new_value !== null && new_value !== undefined) { + if (ref_on_change_vals !== undefined && $.inArray(new_value, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { return; } text_input_elt.attr('value', new_value); --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scr ollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).bind("click",c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d);return a}function show_hide_popupmenu_options(d,c,a){var a=(a===undefined?true:a);var b=new RegExp(c);$(d).find("li").each(function(){if(b.exec($(this).text())){if(a){$(this).show()}else{$(this).hide()}}})}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("ta rget");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));a.find("a").bind("click",function(b){b.stopPropagation();return true});make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c. attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).rem ove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is (":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c =$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.lo g_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c) ===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); +if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scr ollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).bind("click",c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d);return a}function show_hide_popupmenu_options(d,c,a){var a=(a===undefined?true:a);var b=new RegExp(c);$(d).find("li").each(function(){if(b.exec($(this).text())){if(a){$(this).show()}else{$(this).hide()}}})}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("ta rget");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));a.find("a").bind("click",function(b){b.stopPropagation();return true});make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c. attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(l!==n&&n!==null&&n!==undefined){if(h!==undefined&&$.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur( function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").cl ick(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function rese t_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};Ga laxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_val ue");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)});

1 0

galaxy-dist commit 243d80d9905a: adding setup_rabbitmq.sh script.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288197416 14400 # Node ID 243d80d9905af9121452f1a0955b2b49c076d66e # Parent 9c6040ab75a8397a5708cfec4edfe216927b8220 adding setup_rabbitmq.sh script. web api minor code fixes --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -91,7 +91,10 @@ def submit( api_key, url, data, return_f except urllib2.HTTPError, e: print e print e.read( 1024 ) - sys.exit( 1 ) + if return_formatted: + sys.exit( 1 ) + else: + return 'Error. '+ str( e ) if not return_formatted: return r print 'Response' --- /dev/null +++ b/setup_rabbitmq.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0` +python scripts/galaxy_messaging/server/setup_rabbitmq.py universe_wsgi.ini --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -184,10 +184,11 @@ class DataTransfer(object): url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, self.server_port, api.encode_id( self.config_id_secret, self.library_id ) ) - log.debug(str((self.api_key, url, data))) + log.debug( str( ( self.api_key, url, data ) ) ) retval = api.submit( self.api_key, url, data, return_formatted=False ) - except: - self.error_and_exit(str(e)) + log.debug( str( retval ) ) + except Exception, e: + self.error_and_exit( str( e ) ) def update_status(self, status, dataset_id='All', msg=''): ''' @@ -212,7 +213,7 @@ class DataTransfer(object): api.encode_id( self.config_id_secret, self.request_id ) ) log.debug(str((self.api_key, url, data))) retval = api.update( self.api_key, url, data, return_formatted=False ) - log.debug('done.') + log.debug( str( retval ) ) except urllib2.URLError, e: log.debug( 'ERROR(sample_dataset_transfer_status (%s)): %s' % ( url, str(e) ) ) log.error(traceback.format_exc()) --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -11,13 +11,17 @@ import os, sys, csv, ConfigParser def main( config_file ): - config = ConfigParser.ConfigParser() - config.read( config_file ) - rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) - username = config.get( 'galaxy_amqp', 'userid' ) - password = config.get( 'galaxy_amqp', 'password' ) - virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) - + try: + config = ConfigParser.ConfigParser() + config.read( config_file ) + rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) + username = config.get( 'galaxy_amqp', 'userid' ) + password = config.get( 'galaxy_amqp', 'password' ) + virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) + except Exception, e: + print 'Fatal error:', str(e) + sys.exit(1) + cmd_list = [ 'add_user %s %s' % ( username, password ), 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ),

1 0

galaxy-dist commit 121be69ca306: Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288197699 14400 # Node ID 121be69ca30675593dc9fc247a4b10a118fed227 # Parent 243d80d9905af9121452f1a0955b2b49c076d66e Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test. --- /dev/null +++ b/test-data/cuffdiff_out8.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out9.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out11.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out6.txt @@ -0,0 +1,88 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 +XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 +XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 +XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 +XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 +XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 +XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 +XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 +XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 +XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 +XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 +XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 +XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 +XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 +XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 +XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 +XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 +XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 +XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 +XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 +XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 +XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 +XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 +XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 +XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 +XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 +XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 +XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 +XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 +XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 +XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 +XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 +XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 +XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 +XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 +XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 +XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 +XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 +XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 +XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 +XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 +XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 +XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 +XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 +XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 +XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 +XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 +XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 +XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 +XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 +XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 +XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 +XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 +XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 +XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 +XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 --- /dev/null +++ b/test-data/cuffdiff_out10.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out7.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out1.txt @@ -0,0 +1,99 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes +TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes +TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no +TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes +TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no +TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no +TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no +TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no +TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes +TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes +TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -73,11 +73,21 @@ <param name="min_mapqual" value="0" ftype="sam" /><param name="min_alignment_count" value="0" ftype="sam" /><param name="sPaired" value="single" ftype="sam" /> - -  -  + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="8"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="4"/> + <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> + <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> + <output name="splicing_diff" file="cuffdiff_out9.txt"/> + <output name="promoters_diff" file="cuffdiff_out10.txt"/> + <output name="cds_diff" file="cuffdiff_out11.txt"/></test></tests> --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -111,13 +111,13 @@ def __main__(): shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds_exp.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_promoters.diff" ), options.promoters_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) except Exception, e: stop_err( 'Error in cuffdiff:\n' + str( e ) ) finally: --- /dev/null +++ b/test-data/cuffdiff_out5.txt @@ -0,0 +1,99 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 +TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 +TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 +TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 +TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 +TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 +TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 +TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 +TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 +TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 +TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 +TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 +TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 +TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 +TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 +TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 +TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 +TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 +TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 +TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 +TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 +TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 +TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 +TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 +TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 +TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 +TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 +TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 +TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 +TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 +TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 +TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 +TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 +TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 +TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 +TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 +TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 +TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 +TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 +TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 +TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 +TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 +TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 +TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 +TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 +TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 +TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 +TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 +TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 +TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 +TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 +TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 +TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 +TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 +TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 +TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 +TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 +TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 +TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 --- a/test-data/cuffdiff_out5.tracking +++ /dev/null @@ -1,2 +0,0 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q0_FPKM q0_conf_lo q0_conf_hi q1_FPKM q1_conf_lo q1_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 67745 0 163551 --- /dev/null +++ b/test-data/cuffdiff_out2.txt @@ -0,0 +1,88 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes +XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes +XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes +XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no --- /dev/null +++ b/test-data/cuffdiff_out3.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out4.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant

1 0

galaxy-dist commit d57ea326563c: More tweaking to try to get Cuffdiff to pass functional tests. The problem is that Cuffdiff's output is not deterministic, so lines_diff needs to be large enough (but no larger than needed) to accomodate small differences in output.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288216747 14400 # Node ID d57ea326563cb4539e47aae49daa6c5dfc69efc5 # Parent 6a97d4fc4268493480a0a3e7462e91f48d926a72 More tweaking to try to get Cuffdiff to pass functional tests. The problem is that Cuffdiff's output is not deterministic, so lines_diff needs to be large enough (but no larger than needed) to accomodate small differences in output. --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -77,7 +77,7 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/><output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>

1 0

galaxy-dist commit 522c99a05163: fixed Lab menu access bug
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288298593 14400 # Node ID 522c99a05163c1816e9fe3be4c0b4ad05bff3ea0 # Parent 7327a60e33968cb067edf6541cc84643f970180d fixed Lab menu access bug fixed rabbitmq setup script bug --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -84,7 +84,7 @@ [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and trans.user.requests ) ) + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types() ) ) ) %> ## Visualization menu. --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -25,7 +25,7 @@ def main( config_file ): cmd_list = [ 'add_user %s %s' % ( username, password ), 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), - 'set_permissions -p %s %s "%s.*" ".*" ".*"' % ( virtual_host, username, username ) + 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username ) ] for cmd in cmd_list:

1 0

galaxy-dist commit 247c19db7f89: fix for the Lab access bug caused by the last commit .
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288299278 14400 # Node ID 247c19db7f8987d9da245bc750043188d4a7c373 # Parent 522c99a05163c1816e9fe3be4c0b4ad05bff3ea0 fix for the Lab access bug caused by the last commit . --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -84,7 +84,7 @@ [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types() ) ) ) + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types( trans ) ) ) ) %> ## Visualization menu.

1 0

galaxy-dist commit a2e4d36c4318: Make fastx_barcode_splitter_galaxy_wrapper.sh invoke bash rather than sh.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288189891 14400 # Node ID a2e4d36c4318bc4ce73af9df869ae4071af33d55 # Parent 0185bb614c7721d6edf6822ad973e589620b91f5 Make fastx_barcode_splitter_galaxy_wrapper.sh invoke bash rather than sh. --- a/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh +++ b/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009 A. Gordon (gordon(a)cshl.edu)

1 0

galaxy-dist commit 6a97d4fc4268: Update test data for GFF-to-BED to accomodate change made in 4475:aaacde471f03.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288198736 14400 # Node ID 6a97d4fc4268493480a0a3e7462e91f48d926a72 # Parent 121be69ca30675593dc9fc247a4b10a118fed227 Update test data for GFF-to-BED to accomodate change made in 4475:aaacde471f03. --- a/test-data/gff2bed_out2.bed +++ b/test-data/gff2bed_out2.bed @@ -1,3 +1,3 @@ -chr1 3204562 3661579 Xkr4 0 - 3204562 3204562 0 3 2487,200,947 0,207220,456070 -chr1 4481008 4486494 Sox17 0 - 4481008 4481008 0 5 1741,367,92,807,123 0,2172,2844,4208,5363 -chr1 4763278 4775807 Mrpl15 0 - 4763278 4763278 0 5 3604,124,166,155,154 0,4327,9370,10753,12375 +chr1 3204562 3661579 Xkr4 0 - 3204562 3661579 0 3 2487,200,947 0,207220,456070 +chr1 4481008 4486494 Sox17 0 - 4481008 4486494 0 5 1741,367,92,807,123 0,2172,2844,4208,5363 +chr1 4763278 4775807 Mrpl15 0 - 4763278 4775807 0 5 3604,124,166,155,154 0,4327,9370,10753,12375

1 0