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commit/galaxy-central: greg: Potential fix for the buildbot.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c04fb09d5d42/ changeset: c04fb09d5d42 user: greg date: 2012-02-29 22:27:46 summary: Potential fix for the buildbot. affected #: 1 file diff -r a412cb08e5ab07488984305628b2eb2d4a97a781 -r c04fb09d5d42a8ba25c81e812845f85692a820d7 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -69,6 +69,7 @@ universe_wsgi.ini.sample tool_data_table_conf.xml.sample tool-data/shared/ucsc/builds.txt.sample +migrated_tools_conf.xml.sample " DIRS=" 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: Style updates for embedded items to reduce visual footprint.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a412cb08e5ab/ changeset: a412cb08e5ab user: jgoecks date: 2012-02-29 18:53:48 summary: Style updates for embedded items to reduce visual footprint. affected #: 4 files diff -r a7fec5917853c921043be653c87dea3ce781452b -r a412cb08e5ab07488984305628b2eb2d4a97a781 static/june_2007_style/blue/embed_item.css --- a/static/june_2007_style/blue/embed_item.css +++ b/static/june_2007_style/blue/embed_item.css @@ -1,5 +1,5 @@ -.embedded-item{margin-top:0.5em;margin-left:auto;margin-right:auto;width:90%;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} -.embedded-item.display {padding: 0.5em;} +.embedded-item{margin:0em auto;width:90%;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} +.embedded-item.display{padding:2px;} .embedded-item.history{background-color:#C1C9E5} .embedded-item.history p{background:#C1C9E5 no-repeat 2px 2px;margin-top:0;margin-bottom:0;} .embedded-item.dataset{background-color:#CFC} @@ -9,9 +9,11 @@ .embedded-item.visualization{background-color:#BBBBBB} .embedded-item.visualization p{background:#BBBBBB no-repeat 2px 2px;margin-top:0;margin-bottom:0;} .embedded-item.placeholder{} -.embedded-item .item-content{max-height:25em;overflow:auto;display:none;} -.embedded-item .title{vertical-align:top;text-align:center;font-weight:bold;} -.embedded-item.placeholder .content{padding: 1em 1em;font-style:italic;text-align:center;} +.embedded-item .expanded-content{display:none;} +.embedded-item .item-content{max-height:25em;overflow:auto;} +.embedded-item.visualization .item-content{overflow:hidden;} +.embedded-item .title{vertical-align:top;text-align:center;font-weight:bold;padding-bottom:2px;} +.embedded-item.placeholder .content{padding: 0.5em 0.5em;font-style:italic;text-align:center;} table.annotated-item{width:100%;border-collapse:collapse;} table.annotated-item td,th{padding:0;} table.annotated-item .annotation{padding-left:2em;width:40%;} diff -r a7fec5917853c921043be653c87dea3ce781452b -r a412cb08e5ab07488984305628b2eb2d4a97a781 static/june_2007_style/embed_item.css.tmpl --- a/static/june_2007_style/embed_item.css.tmpl +++ b/static/june_2007_style/embed_item.css.tmpl @@ -1,16 +1,13 @@ - -.embedded-item { - margin-top: 0.5em - margin-left:auto; - margin-right:auto; - width:90%; - -moz-border-radius:0.5em; - -webkit-border-radius:0.5em; - border-radius:0.5em; +.embedded-item { + margin: 0em auto; + width: 90%; + -moz-border-radius: 0.5em; + -webkit-border-radius: 0.5em; + border-radius: 0.5em; } .embedded-item.display { - padding: 0.5em; + padding: 2px; } .embedded-item.history { @@ -54,39 +51,47 @@ .embedded-item.placeholder{} +.embedded-item .expanded-content { + display: none; +} + .embedded-item .item-content { max-height: 25em; overflow: auto; - display: none; +} + +.embedded-item.visualization .item-content { + overflow: hidden; } .embedded-item .title { - vertical-align:top; - text-align:center; + vertical-align: top; + text-align: center; font-weight: bold; + padding-bottom: 2px; } .embedded-item.placeholder .content { - padding: 1em 1em; - font-style:italic; - text-align:center; + padding: 0.5em 0.5em; + font-style: italic; + text-align: center; } table.annotated-item { - width:100%; - border-collapse:collapse; + width: 100%; + border-collapse: collapse; } table.annotated-item td,th { - padding:0; + padding: 0; } table.annotated-item .annotation { - padding-left:2em; - width:40%; + padding-left: 2em; + width: 40%; } table.annotated-item td.annotation { - vertical-align:text-top; - padding-top:1em; + vertical-align: text-top; + padding-top: 1em; } \ No newline at end of file diff -r a7fec5917853c921043be653c87dea3ce781452b -r a412cb08e5ab07488984305628b2eb2d4a97a781 templates/embed_base.mako --- a/templates/embed_base.mako +++ b/templates/embed_base.mako @@ -9,12 +9,13 @@ <div class='embedded-item display ${get_class_display_name( item.__class__ ).lower()}'><div class='title'> ${self.render_title( item )} - <hr/></div><div class='summary-content'> ${self.render_summary_content( item, item_data )} </div> - <div class='item-content'> + <div class='expanded-content'> + <hr/> + <div class='item-content'></div></div></div> diff -r a7fec5917853c921043be653c87dea3ce781452b -r a412cb08e5ab07488984305628b2eb2d4a97a781 templates/page/display.mako --- a/templates/page/display.mako +++ b/templates/page/display.mako @@ -24,7 +24,8 @@ error: function() { alert("Getting item content failed."); }, success: function( item_content ) { container.find(".summary-content").hide("fast"); - container.find(".item-content").html(item_content).show("fast"); + container.find(".item-content").html(item_content); + container.find(".expanded-content").show("fast"); container.find(".toggle-expand").hide(); container.find(".toggle").show(); @@ -41,7 +42,7 @@ }); } else { container.find(".summary-content").hide("fast"); - container.find(".item-content").show("fast"); + container.find(".expanded-content").show("fast"); container.find(".toggle-expand").hide(); container.find(".toggle").show(); } @@ -49,7 +50,7 @@ // Hide embedded item. var hide_embedded_item = function() { - container.find(".item-content").hide("fast"); + container.find(".expanded-content").hide("fast"); container.find(".summary-content").show("fast"); container.find(".toggle").hide(); container.find(".toggle-expand").show(); @@ -72,7 +73,7 @@ // Setup toggle embed. var toggle_embed = $(this).find('.toggle-embed'); toggle_embed.click( function() { - if (container.find(".item-content").is(":visible")) { + if (container.find(".expanded-content").is(":visible")) { hide_embedded_item(); } else { show_embedded_item(); 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: Cloud launch basics.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a7fec5917853/ changeset: a7fec5917853 user: dannon date: 2012-02-29 17:58:22 summary: Cloud launch basics. TODO: Tons of help text, shift instance dns wait to page level. pkey direct download. affected #: 11 files diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -216,11 +216,7 @@ self.tool_runners = [] self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Cloud configuration options - self.cloud_controller_instance = string_as_bool( kwargs.get( 'cloud_controller_instance', 'False' ) ) - if self.cloud_controller_instance == True: - self.enable_cloud_execution = string_as_bool( kwargs.get( 'enable_cloud_execution', 'True' ) ) - else: - self.enable_cloud_execution = string_as_bool( kwargs.get( 'enable_cloud_execution', 'False' ) ) + self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) # Galaxy messaging (AMQP) configuration options self.amqp = {} try: diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1671,58 +1671,11 @@ self.galaxy_session = galaxy_session self.history = history -class CloudImage( object ): - def __init__( self ): - self.id = None - self.instance_id = None - self.state = None - class UCI( object ): def __init__( self ): self.id = None self.user = None -class CloudInstance( object ): - def __init__( self ): - self.id = None - self.user = None - self.name = None - self.instance_id = None - self.mi = None - self.state = None - self.public_dns = None - self.availability_zone = None - -class CloudStore( object ): - def __init__( self ): - self.id = None - self.volume_id = None - self.user = None - self.size = None - self.availability_zone = None - -class CloudSnapshot( object ): - def __init__( self ): - self.id = None - self.user = None - self.store_id = None - self.snapshot_id = None - -class CloudProvider( object ): - def __init__( self ): - self.id = None - self.user = None - self.type = None - -class CloudUserCredentials( object ): - def __init__( self ): - self.id = None - self.user = None - self.name = None - self.accessKey = None - self.secretKey = None - self.credentials = [] - class StoredWorkflow( object, APIItem): api_collection_visible_keys = ( 'id', 'name' ) api_element_visible_keys = ( 'id', 'name' ) diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b lib/galaxy/web/controllers/cloud.py --- /dev/null +++ b/lib/galaxy/web/controllers/cloud.py @@ -0,0 +1,215 @@ +""" +Cloud Controller: handles all cloud interactions. + +Adapted from Brad Chapman and Enis Afgan's BioCloudCentral +BioCloudCentral Source: https://github.com/chapmanb/biocloudcentral + +""" + +import boto +import datetime +import logging +import time +from galaxy import web +from galaxy.web.base.controller import BaseUIController +from boto.ec2.regioninfo import RegionInfo +from boto.exception import EC2ResponseError + +log = logging.getLogger(__name__) + +class CloudController(BaseUIController): + def __init__(self, app): + BaseUIController.__init__(self, app) + + @web.expose + def index(self, trans): + return trans.fill_template("cloud/index.mako") + + @web.expose + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type): + ec2_error = None + try: + # Create security group & key pair used when starting an instance + ec2_conn = connect_ec2(key_id, secret) + sg_name = create_cm_security_group(ec2_conn) + kp_name, kp_material = create_key_pair(ec2_conn) + except EC2ResponseError, err: + ec2_error = err.error_message + if ec2_error: + return trans.fill_template("cloud/run.mako", error = ec2_error) + else: + rs = run_instance(ec2_conn=ec2_conn, + user_provided_data={'cluster_name':cluster_name, + 'password':password, + 'access_key':key_id, + 'secret_key':secret, + 'instance_type':instance_type}, + key_name=kp_name, + security_groups=[sg_name]) + if rs: + instance = rs.instances[0] + ct = 0 + while not instance.public_dns_name: + # Can take a second to have public dns name registered. + # DBTODO, push this into a page update, this is not ideal. + instance.update() + ct +=1 + time.sleep(1) + return trans.fill_template("cloud/run.mako", + instance = rs.instances[0], + kp_name = kp_name, + kp_material = kp_material) + else: + return trans.fill_template("cloud/run.mako", + error = "Instance failure, but no specific error was detected. Please check your AWS Console.") + +# ## Cloud interaction methods +def connect_ec2(a_key, s_key): + """ Create and return an EC2 connection object. + """ + # Use variables for forward looking flexibility + # AWS connection values + region_name = 'us-east-1' + region_endpoint = 'ec2.amazonaws.com' + is_secure = True + ec2_port = None + ec2_conn_path = '/' + r = RegionInfo(name=region_name, endpoint=region_endpoint) + ec2_conn = boto.connect_ec2(aws_access_key_id=a_key, + aws_secret_access_key=s_key, + api_version='2011-11-01', # needed for availability zone support + is_secure=is_secure, + region=r, + port=ec2_port, + path=ec2_conn_path) + return ec2_conn + +def create_cm_security_group(ec2_conn, sg_name='CloudMan'): + """ Create a security group with all authorizations required to run CloudMan. + If the group already exists, check its rules and add the missing ones. + Return the name of the created security group. + """ + cmsg = None + # Check if this security group already exists + sgs = ec2_conn.get_all_security_groups() + for sg in sgs: + if sg.name == sg_name: + cmsg = sg + log.debug("Security group '%s' already exists; will add authorizations next." % sg_name) + break + # If it does not exist, create security group + if cmsg is None: + log.debug("Creating Security Group %s" % sg_name) + cmsg = ec2_conn.create_security_group(sg_name, 'A security group for CloudMan') + # Add appropriate authorization rules + # If these rules already exist, nothing will be changed in the SG + ports = (('80', '80'), # Web UI + ('20', '21'), # FTP + ('22', '22'), # ssh + ('30000', '30100'), # FTP transfer + ('42284', '42284')) # CloudMan UI + for port in ports: + try: + if not rule_exists(cmsg.rules, from_port=port[0], to_port=port[1]): + cmsg.authorize(ip_protocol='tcp', from_port=port[0], to_port=port[1], cidr_ip='0.0.0.0/0') + else: + log.debug("Rule (%s:%s) already exists in the SG" % (port[0], port[1])) + except EC2ResponseError, e: + log.error("A problem with security group authorizations: %s" % e) + # Add rule that allows communication between instances in the same SG + g_rule_exists = False # Flag to indicate if group rule already exists + for rule in cmsg.rules: + for grant in rule.grants: + if grant.name == cmsg.name: + g_rule_exists = True + log.debug("Group rule already exists in the SG") + if g_rule_exists: + break + if g_rule_exists is False: + try: + cmsg.authorize(src_group=cmsg) + except EC2ResponseError, e: + log.error("A problem w/ security group authorization: %s" % e) + log.info("Done configuring '%s' security group" % cmsg.name) + return cmsg.name + +def rule_exists(rules, from_port, to_port, ip_protocol='tcp', cidr_ip='0.0.0.0/0'): + """ A convenience method to check if an authorization rule in a security + group exists. + """ + for rule in rules: + if rule.ip_protocol == ip_protocol and rule.from_port == from_port and \ + rule.to_port == to_port and cidr_ip in [ip.cidr_ip for ip in rule.grants]: + return True + return False + +def create_key_pair(ec2_conn, key_name='cloudman_key_pair'): + """ Create a key pair with the provided name. + Return the name of the key or None if there was an error creating the key. + """ + kp = None + # Check if a key pair under the given name already exists. If it does not, + # create it, else return. + kps = ec2_conn.get_all_key_pairs() + for akp in kps: + if akp.name == key_name: + log.debug("Key pair '%s' already exists; not creating it again." % key_name) + return akp.name, None + try: + kp = ec2_conn.create_key_pair(key_name) + except EC2ResponseError, e: + log.error("Problem creating key pair '%s': %s" % (key_name, e)) + return None, None + return kp.name, kp.material + +def run_instance(ec2_conn, user_provided_data, image_id='ami-da58aab3', + kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair', + security_groups=['CloudMan']): + """ Start an instance. If instance start was OK, return the ResultSet object + else return None. + """ + rs = None + instance_type = user_provided_data['instance_type'] + # Remove 'instance_type' key from the dict before creating user data + del user_provided_data['instance_type'] + placement = _find_placement(ec2_conn, instance_type) + ud = "\n".join(['%s: %s' % (key, value) for key, value in user_provided_data.iteritems() if key != 'kp_material']) + try: + rs = ec2_conn.run_instances(image_id=image_id, + instance_type=instance_type, + key_name=key_name, + security_groups=security_groups, + user_data=ud, + kernel_id=kernel_id, + ramdisk_id=ramdisk_id, + placement=placement) + except EC2ResponseError, e: + log.error("Problem starting an instance: %s" % e) + if rs: + try: + log.info("Started an instance with ID %s" % rs.instances[0].id) + except Exception, e: + log.error("Problem with the started instance object: %s" % e) + else: + log.warning("Problem starting an instance?") + return rs + +def _find_placement(ec2_conn, instance_type): + """Find a region zone that supports our requested instance type. + + We need to check spot prices in the potential availability zones + for support before deciding on a region: + + http://blog.piefox.com/2011/07/ec2-availability-zones-and-instance.html + """ + base = ec2_conn.region.name + yesterday = datetime.datetime.now() - datetime.timedelta(1) + for loc_choice in ["b", "a", "c", "d"]: + cur_loc = "{base}{ext}".format(base=base, ext=loc_choice) + if len(ec2_conn.get_spot_price_history(instance_type=instance_type, + end_time=yesterday.isoformat(), + availability_zone=cur_loc)) > 0: + return cur_loc + log.error("Did not find availabilty zone in {0} for {1}".format(base, instance_type)) + return None + diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -481,7 +481,15 @@ trans.sa_session.flush() return trans.show_message( "<p>Secondary dataset has been made primary.</p>", refresh_frames=['history'] ) except: - return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) + return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) + + @web.expose + def bucket_proxy( self, trans, bucket=None, **kwd): + if bucket: + trans.response.set_content_type( 'text/xml' ) + b_list_xml = urllib.urlopen('http://s3.amazonaws.com/%s/' % bucket) + return b_list_xml.read() + raise Exception("You must specify a bucket") # ---- Debug methods ---------------------------------------------------- @@ -496,7 +504,7 @@ if isinstance( kwd[k], FieldStorage ): rval += "-> %s" % kwd[k].file.read() return rval - + @web.expose def generate_error( self, trans ): raise Exception( "Fake error!" ) diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b templates/cloud/index.mako --- /dev/null +++ b/templates/cloud/index.mako @@ -0,0 +1,94 @@ +<%inherit file="/webapps/galaxy/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="shared" + self.message_box_visible=False +%> +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "autocomplete_tagging" )} + <style type="text/css"> + #new_history_p{ + line-height:2.5em; + margin:0em 0em .5em 0em; + } + #new_history_cbx{ + margin-right:.5em; + } + #new_history_input{ + display:none; + line-height:1em; + } + #ec_button_container{ + float:right; + } + div.toolForm{ + margin-top: 10px; + margin-bottom: 10px; + } + div.toolFormTitle{ + cursor:pointer; + } + .title_ul_text{ + text-decoration:underline; + } + .step-annotation { + margin-top: 0.25em; + font-weight: normal; + font-size: 97%; + } + .workflow-annotation { + margin-bottom: 1em; + } + </style> +</%def> + + + + +<%def name="center_panel()"> + <div style="overflow: auto; height: 100%;"> + <div class="page-container" style="padding: 10px;"> + <h2>Launch a Galaxy Cloud Instance</h2> + <div class="toolForm"> + <form action="cloud/launch_instance" method="post"> + <div class="form-row"> + <label for="id_cluster_name">Cluster Name</label> + <input type="text" size="80" name="cluster_name" id="id_cluster_name"/><br/> + </div> + <div class="form-row"> + <label for="id_password">Password</label> + <input type="password" size="40" name="password" id="id_password"/><br/> + </div> + <div class="form-row"> + <label for="id_key_id">Key ID</label> + <input type="text" size="40" name="key_id" id="id_key_id"/><br/> + </div> + <div class="form-row"> + <label for="id_secret">Secret Key</label> + <input type="text" size="120" name="secret" id="id_secret"/><br/> + </div> + <div class="form-row"> + <label for="id_instance_type">Instance Type</label> + <select name="instance_type" id="id_instance_type"> + <option value="m1.large">Large</option> + <option value="t1.micro">Micro</option> + <option value="m1.xlarge">Extra Large</option> + <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> + </select> + </div> + <div class="form-row"> + <p>Requesting the instance may take a moment, please be patient. Do not refresh your browser or navigate away from the page</p> + <input type="submit" value="Submit" id="id_submit"/> + </div> + </form> + </div> + </div> + </div> +</%def> + diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b templates/cloud/run.mako --- /dev/null +++ b/templates/cloud/run.mako @@ -0,0 +1,41 @@ +<%inherit file="/webapps/galaxy/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="shared" + self.message_box_visible=False +%> +</%def> + + +<%def name="center_panel()"> + <div style="overflow: auto; height: 100%;"> + <div class="page-container" style="padding: 10px;"> + <h2>Launching a Galaxy Cloud Instance</h2> +%if error: + <p>${error}</p> +%elif instance: + %if kp_material: + <h3>Very Important Key Pair Information</h3> + <p>A new key pair named '${kp_name}' has been created in your AWS + account and will be used to access this instance via ssh. It is + <strong>very important</strong> that you save the following private key + as it is not saved on this Galaxy instance and will be permanently lost + once you leave this page. To do this, save the following key block as + a plain text file named '${kp_name}'.</p> + <pre>${kp_material}</pre> + %endif + <p>The instance '${instance.id} has been successfully launched using the + '${instance.image_id}' AMI.<br/> Access it at <a + href="http://${instance.public_dns_name}">http://${instance.public_dns_name}</a></p> + <p>SSH access is available using your private key '${kp_name}'.</p> +%else: + <p> Unknown failure, no instance. Please refer to your AWS console at <a + href="https://console.aws.amazon.com">https://console.aws.amazon.com</a></p> +%endif + </div> + </div> +</%def> + diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -184,14 +184,9 @@ <%def name="init()"><% - if trans.app.config.cloud_controller_instance: - self.has_left_panel=False - self.has_right_panel=False - self.active_view="cloud" - else: - self.has_left_panel=True - self.has_right_panel=True - self.active_view="analysis" + self.has_left_panel = True + self.has_right_panel = True + self.active_view = "analysis" %> %if trans.app.config.require_login and not trans.user: <script type="text/javascript"> @@ -228,8 +223,6 @@ center_url = h.url_for( controller='workflow', action='run', id=workflow_id ) elif m_c is not None: center_url = h.url_for( controller=m_c, action=m_a ) - elif trans.app.config.cloud_controller_instance: - center_url = h.url_for( controller='cloud', action='list' ) else: center_url = h.url_for( '/static/welcome.html' ) %> diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -105,6 +105,16 @@ %> %endif + ## Cloud menu. + %if app.config.get_bool( 'enable_cloud_control', False ): + <% + menu_options = [ + [_('New Cloud Cluster'), h.url_for( controller='/cloud', action='index' ) ], + ] + tab( "cloud", _("Cloud"), h.url_for( controller='/cloud', action='index'), menu_options=menu_options ) + %> + %endif + ## Admin tab. ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -61,12 +61,11 @@ </div></%def> - <%def name="render_item_links( workflow )"> %if workflow.importable: - <a + <a href="${h.url_for( controller='/workflow', action='imp', id=trans.security.encode_id(workflow.id) )}" - class="icon-button import" + class="icon-button import" ## Needed to overwide initial width so that link is floated left appropriately. style="width: 100%" title="Import workflow">Import workflow</a> diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b templates/workflow/run.mako --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -252,7 +252,15 @@ if not enable_unique_defaults: del already_used[:] %> - ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + %if step.type == None: + ##Input Dataset Step, wrap for multiinput. + <span class='multiinput_wrap'> + ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + </span> + %else: + ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + %endif + <input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" /> %endif %elif isinstance( value, RuntimeValue ) or ( str(step.id) + '|__runtime__' + prefix + param.name ) in incoming: diff -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 -r a7fec5917853c921043be653c87dea3ce781452b universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -251,6 +251,10 @@ # Note that this requires java > 1.4 for executing yuicompressor.jar #pack_scripts = False +# Enable Cloud Launch + +#enable_cloud_launch = False + # -- Advanced proxy features # For help on configuring the Advanced proxy features, see: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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2 1

commit/galaxy-central: greg: Fixes for installing tool shed repositories that contain tools when done by the InstallManager, and loading the tool panel with tools in an installed repository.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a86a94f46c6c/ changeset: a86a94f46c6c user: greg date: 2012-02-29 17:34:10 summary: Fixes for installing tool shed repositories that contain tools when done by the InstallManager, and loading the tool panel with tools in an installed repository. affected #: 3 files diff -r 9f623fc8e798e32bdc80bc5166448ed1273c373e -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -116,19 +116,25 @@ changeset_revision, tmp_name ): # Generate the metadata for the installed tool shed repository, among other things. It is critical that the installed repository is # updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. - tool_panel_dict = {} + tool_panel_dict_for_display = {} + tool_panel_dict_for_metadata = {} for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) + guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) # See if tool_config is defined somewhere in self.proprietary_tool_panel_elems. is_loaded, tool_section = self.get_containing_tool_section( tool_config ) + tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_section=tool_section ) + # The tool_panel_dict_for_tool_config dictionary contains a single entry that looks something like this. + # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # Add the new entry to the dictionary we're defining to set metadata. + for k, v in tool_panel_dict_for_tool_config.items(): + tool_panel_dict_for_metadata[ k ] = v if is_loaded: - guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) - tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_section=tool_section ) - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # Add the new entry to the dictionary we're defining to set the tool panel display. for k, v in tool_panel_dict_for_tool_config.items(): - tool_panel_dict[ k ] = v - metadata_dict = generate_metadata( self.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict ) + tool_panel_dict_for_display[ k ] = v + metadata_dict = generate_metadata( self.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict_for_metadata ) # Add a new record to the tool_shed_repository table if one doesn't already exist. If one exists but is marked # deleted, undelete it. It is critical that this happens before the call to add_to_tool_panel() below because # tools will not be properly loaded if the repository is marked deleted. @@ -157,7 +163,7 @@ repository_tools_tups, self.repository_owner, self.migrated_tools_config, - tool_panel_dict, + tool_panel_dict=tool_panel_dict_for_display, new_install=True ) # Remove the temporary file try: diff -r 9f623fc8e798e32bdc80bc5166448ed1273c373e -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -189,14 +189,14 @@ tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) if section: # This means all tools are loaded into the same tool panel section or are all outside of any sections. - for guid, tool_section_dict in tool_panel_dict.items(): + for tool_panel_dict_guid, tool_section_dict in tool_panel_dict.items(): if tool_section_dict [ 'id' ] != section.id or \ tool_section_dict [ 'version' ] != section.version or \ tool_section_dict [ 'name' ] != section.name: tool_section_dict [ 'id' ] = section.id tool_section_dict [ 'version' ] = section.version tool_section_dict [ 'name' ] = section.name - tool_panel_dict[ guid ] = tool_section_dict + tool_panel_dict[ tool_panel_dict_guid ] = tool_section_dict update_needed = True else: # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. @@ -1986,7 +1986,6 @@ Find extra files in the job working directory and move them into the appropriate dataset's files directory """ - # print "Working in collect_associated_files" for name, hda in output.items(): temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) try: diff -r 9f623fc8e798e32bdc80bc5166448ed1273c373e -r a86a94f46c6cad83eabf76aa20fb3537ddda4ee1 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -18,14 +18,14 @@ index, shed_tool_conf_dict = get_shed_tool_conf_dict( app, shed_tool_conf ) tool_path = shed_tool_conf_dict[ 'tool_path' ] config_elems = shed_tool_conf_dict[ 'config_elems' ] - # Generate the list of ElementTree Element objects for each section or list of tools. + # Generate the list of ElementTree Element objects for each section or tool. elem_list = generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, repository_tools_tups, owner=owner ) - # Load the tools into the tool panel outside of any sections. + # Load the tools into the tool panel. for config_elem in elem_list: if config_elem.tag == 'section': app.toolbox.load_section_tag_set( config_elem, app.toolbox.tool_panel, tool_path ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: jgoecks: Fix incorrect sniffing for encodepeak datatype.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9f623fc8e798/ changeset: 9f623fc8e798 user: jgoecks date: 2012-02-29 16:42:40 summary: Fix incorrect sniffing for encodepeak datatype. affected #: 1 file diff -r 7c75c62bb5822f0cdf38d4800754e424af3d1c74 -r 9f623fc8e798e32bdc80bc5166448ed1273c373e lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -1289,7 +1289,7 @@ MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) def sniff( self, filename ): - return Exception( "Unimplemented Function" ) + return False def get_track_type( self ): return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} 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.

1 0

commit/galaxy-central: jgoecks: Fix background for embedded visualizations.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7c75c62bb582/ changeset: 7c75c62bb582 user: jgoecks date: 2012-02-29 16:35:49 summary: Fix background for embedded visualizations. affected #: 2 files diff -r 25510b48015adfccb5826047b574f4a312f1ad6c -r 7c75c62bb5822f0cdf38d4800754e424af3d1c74 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -1,4 +1,4 @@ -.viewport-container{overflow-x:hidden;overflow-y:auto;} +.viewport-container{overflow-x:hidden;overflow-y:auto;background:white;} .nav-container{width:100%;} .nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;background-image:url(panel_header_bg.png);background-position:middle center;background-repeat:repeat-x;border-bottom:solid #333 1px;} .content{font:10px verdana;} diff -r 25510b48015adfccb5826047b574f4a312f1ad6c -r 7c75c62bb5822f0cdf38d4800754e424af3d1c74 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -1,6 +1,7 @@ .viewport-container { overflow-x: hidden; overflow-y: auto; + background: white; } .nav-container { width: 100%; 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.

1 0

commit/galaxy-central: dan: Fix missing gatk_report datatype in datatypes_conf.xml.sample.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/25510b48015a/ changeset: 25510b48015a user: dan date: 2012-02-29 16:27:49 summary: Fix missing gatk_report datatype in datatypes_conf.xml.sample. affected #: 1 file diff -r fced200b6f153aca87f8e54979daea7fe6370045 -r 25510b48015adfccb5826047b574f4a312f1ad6c datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -102,7 +102,7 @@ <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/></datatype><datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> - <datatype extension="gatk_table" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_report" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/><datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/><datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/><datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> 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.

1 0

commit/galaxy-central: jgoecks: Enable Pages and Trackster by default in universe.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fced200b6f15/ changeset: fced200b6f15 user: jgoecks date: 2012-02-29 15:53:56 summary: Enable Pages and Trackster by default in universe. affected #: 1 file diff -r 41b1080c48b9bf7e8cf70aea97987f7f026e911a -r fced200b6f153aca87f8e54979daea7fe6370045 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -460,13 +460,13 @@ #enable_sequencer_communication = False # Enable Galaxy's built-in visualization module, Trackster. -#enable_tracks = False +#enable_tracks = True # Enable Galaxy Pages. Pages are custom webpages that include embedded Galaxy items, # such as datasets, histories, workflows, and visualizations; pages are useful for # documenting and sharing multiple analyses or workflows. Pages are created using a # WYSIWYG editor that is very similar to a word processor. -#enable_pages = False +#enable_pages = True # Enable authentication via OpenID. Allows users to log in to their Galaxy # account by authenticating with an OpenID provider. 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.

1 0

commit/galaxy-central: dan: Headers, which are important, are kept. Original ordering, which may be specifically needed by tools or external display applications is also maintained.
by Bitbucket 29 Feb '12

29 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/41b1080c48b9/ changeset: 41b1080c48b9 user: dan date: 2012-02-29 15:36:03 summary: Headers, which are important, are kept. Original ordering, which may be specifically needed by tools or external display applications is also maintained. affected #: 2 files diff -r c754d8c07440e4376853eb3b804af366b1442ff0 -r 41b1080c48b9bf7e8cf70aea97987f7f026e911a lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py @@ -0,0 +1,24 @@ +#!/usr/bin/env python + +""" +Uses pysam to bgzip a vcf file as-is. +Headers, which are important, are kept. +Original ordering, which may be specifically needed by tools or external display applications, is also maintained. + +usage: %prog in_file out_file +""" + +from galaxy import eggs +import pkg_resources; pkg_resources.require( "pysam" ) +import ctabix, optparse + +def main(): + # Read options, args. + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + input_fname, output_fname = args + + ctabix.tabix_compress(input_fname, output_fname, force=True) + +if __name__ == "__main__": + main() diff -r c754d8c07440e4376853eb3b804af366b1442ff0 -r 41b1080c48b9bf7e8cf70aea97987f7f026e911a lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml --- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml @@ -1,6 +1,6 @@ -<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.0" hidden="true"> +<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.1" hidden="true"> - <command interpreter="python">bgzip.py -P vcf $input1 $output1</command> + <command interpreter="python">vcf_to_vcf_bgzip.py '$input1' '$output1'</command><inputs><page><param format="vcf" name="input1" type="data" label="Choose Vcf file"/> 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.

1 0

commit/galaxy-central: jgoecks: Parameterize per-tool job runners so that parameter name/value pairs can be used to define multiple runners per tool. Documentation is in sample universe file. Add 'params' column to jobs table to store job parameters, and add source parameter for all jobs initiated in Trackster.
by Bitbucket 28 Feb '12

28 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c754d8c07440/ changeset: c754d8c07440 user: jgoecks date: 2012-02-28 23:50:26 summary: Parameterize per-tool job runners so that parameter name/value pairs can be used to define multiple runners per tool. Documentation is in sample universe file. Add 'params' column to jobs table to store job parameters, and add source parameter for all jobs initiated in Trackster. affected #: 8 files diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -180,9 +180,38 @@ # Heartbeat log file name override if global_conf is not None: self.heartbeat_log = global_conf.get( 'heartbeat_log', 'heartbeat.log' ) - #Store per-tool runner config + #Store per-tool runner configs. try: - self.tool_runners = global_conf_parser.items("galaxy:tool_runners") + tool_runners_config = global_conf_parser.items("galaxy:tool_runners") + + # Process config to group multiple configs for the same tool. + tool_runners = {} + for entry in tool_runners_config: + tool_config, url = entry + tool = None + runner_dict = {} + if tool_config.find("[") != -1: + # Found tool with additional params; put params in dict. + tool, params = tool_config[:-1].split( "[" ) + param_dict = {} + for param in params.split( "," ): + name, value = param.split( "@" ) + param_dict[ name ] = value + runner_dict[ 'params' ] = param_dict + else: + tool = tool_config + + # Add runner URL. + runner_dict[ 'url' ] = url + + # Create tool entry if necessary. + if tool not in tool_runners: + tool_runners[ tool ] = [] + + # Add entry to runners. + tool_runners[ tool ].append( runner_dict ) + + self.tool_runners = tool_runners except ConfigParser.NoSectionError: self.tool_runners = [] self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -336,12 +336,15 @@ self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) + self.params = None + if job.params: + self.params = from_json_string( job.params ) self.__user_system_pwent = None self.__galaxy_system_pwent = None def get_job_runner( self ): - return self.tool.job_runner + return self.tool.get_job_runner( self.params ) def get_job( self ): return self.sa_session.query( model.Job ).get( self.job_id ) diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -420,7 +420,8 @@ Column( "job_runner_name", String( 255 ) ), Column( "job_runner_external_id", String( 255 ) ), Column( "object_store_id", TrimmedString( 255 ), index=True ), - Column( "imported", Boolean, default=False, index=True ) ) + Column( "imported", Boolean, default=False, index=True ), + Column( "params", TrimmedString(255), index=True ) ) JobParameter.table = Table( "job_parameter", metadata, Column( "id", Integer, primary_key=True ), diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/model/migrate/versions/0093_add_job_params_col.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0093_add_job_params_col.py @@ -0,0 +1,49 @@ +""" +Migration script to create "params" column in job table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +# Column to add. +params_col = Column( "params", TrimmedString(255), index=True ) + +def display_migration_details(): + print "" + print "This migration script adds a 'params' column to the Job table." + +def upgrade(): + print __doc__ + metadata.reflect() + + # Add column to Job table. + try: + Job_table = Table( "job", metadata, autoload=True ) + params_col.create( Job_table ) + assert params_col is Job_table.c.params + + except Exception, e: + print str(e) + log.debug( "Adding column 'params' to job table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop column from Job table. + try: + Job_table = Table( "job", metadata, autoload=True ) + params_col = Job_table.c.params + params_col.drop() + except Exception, e: + log.debug( "Dropping column 'params' from job table failed: %s" % ( str( e ) ) ) \ No newline at end of file diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -562,6 +562,31 @@ if tool_version: return tool_version.get_version_ids( self.app ) return [] + def get_job_runner( self, job_params=None ): + # Look through runners to find one with matching parameters. + selected_runner = None + if len( self.job_runners ) == 1: + # Most tools have a single runner. + selected_runner = self.job_runners[0] + elif job_params is None: + # Use job runner with no params + for runner in self.job_runners: + if "params" not in runner: + selected_runner = runner + else: + # Find runner with matching parameters. + for runner in self.job_runners: + if "params" in runner: + match = True + runner_params = runner[ "params" ] + for param, value in job_params.items(): + if param not in runner_params or \ + runner_params[ param ] != job_params[ param ]: + match = False + break + if match: + selected_runner = runner + return selected_runner[ "url" ] def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -626,17 +651,18 @@ self.parallelism = ToolParallelismInfo(parallelism) else: self.parallelism = None + # Set job runner(s). Each runner is a dict with 'url' and, optionally, 'params'. if self.app.config.start_job_runners is None: # Jobs are always local regardless of tool config if no additional # runners are started - self.job_runner = "local:///" + self.job_runners = [ { "url" : "local:///" } ] else: # Set job runner to the cluster default - self.job_runner = self.app.config.default_cluster_job_runner - for tup in self.app.config.tool_runners: - if tup[0] == self.id.lower(): - self.job_runner = tup[1] - break + self.job_runners = [ { "url" : self.app.config.default_cluster_job_runner } ] + # Set custom runner(s) if they're defined. + self_id = self.id.lower() + if self_id in self.app.config.tool_runners: + self.job_runners = self.app.config.tool_runners[ self_id ] # Is this a 'hidden' tool (hidden in tool menu) self.hidden = util.xml_text(root, "hidden") if self.hidden: self.hidden = util.string_as_bool(self.hidden) diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -1,6 +1,7 @@ from galaxy.model import LibraryDatasetDatasetAssociation from galaxy.util.bunch import Bunch from galaxy.util.odict import odict +from galaxy.util.json import to_json_string from galaxy.tools.parameters import * from galaxy.tools.parameters.grouping import * from galaxy.util.template import fill_template @@ -100,7 +101,7 @@ tool.visit_inputs( param_values, visitor ) return input_datasets - def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, set_output_history=True, history=None ): + def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, set_output_history=True, history=None, job_params=None ): """ Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use @@ -389,6 +390,8 @@ for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) job.object_store_id = object_store_id + if job_params: + job.params = to_json_string( job_params ) trans.sa_session.add( job ) trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -991,7 +991,9 @@ # Execute tool and handle outputs. # try: - subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=target_history ) + subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, + history=target_history, + job_params={ "source" : "trackster" } ) except Exception, e: # Lots of things can go wrong when trying to execute tool. return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) diff -r c7ca68b622823d146fac4db1cb0d5963e1daa1a9 -r c754d8c07440e4376853eb3b804af366b1442ff0 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -630,8 +630,13 @@ # ---- Tool Job Runners ----------------------------------------------------- -# Individual per-tool job runner overrides. If not listed here, a tool will -# run with the runner defined with default_cluster_job_runner. +# Individual per-tool job runner overrides. Parameters can be included to define +# multiple runners per tool. E.g. to run Cufflinks jobs initiated from Trackster +# differently than standard Cufflinks jobs: +# cufflinks = local:/// +# cufflinks[source@trackster] = local:/// +# If not listed here, a tool will run with the runner defined with +# default_cluster_job_runner. [galaxy:tool_runners] 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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