December 2012 - galaxy-dev - lists.galaxyproject.org

Trying to Run MegaBlast
by greg 11 Dec '12

11 Dec '12

I have a fresh install on our cluster. I'm trying to test out the Megablast tool. The problem is that nothing is listed under "against target database". Where do I get the target databases and how do I tell galaxy about them? Thanks, Greg Here's what the tool looks like: Megablast (version 1.2.0) Compare these sequences: against target database: using word size: Size of best perfect match (-word_size) report hits above this identity (-perc_identity): no cutoff if 0 set expectation value cutoff (-evalue): Filter out low complexity regions? (-dust):

3 4

Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
by Sachit Adhikari 11 Dec '12

11 Dec '12

Hello Everyone, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit

1 0

Installation issue on EC2
by Fabiano Lucchese 11 Dec '12

11 Dec '12

Hi, all. I've been trying to deploy a CloudMan/Galaxy cluster on EC2 for a couple of days now and have been facing all kinds of unexpected weirdness's. I found out that the web-based form that automatically creates the EC2 instance uses an image that doesn`t seem to be officially supported (or at least encouraged) by the Galaxy team, so I decided to launch the instance by hand following the instructions from here: http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted Up to the point before accessing Galaxy, everything looks ok, but the service never starts. Instead, it shows up at the CloudMan Admin page as "Error" and nothing happens if I try to Stop/Start or Restart it.There's no log either. The Postgres service displays an immutable "Starting" status, while its log provides the following message: FATAL: database files are incompatible with server DETAIL: The data directory was initialized by PostgreSQL version 9.1, which is not compatible with this version 8.4.7. It does look like a messed up installation, which is quite surprising as this is supposed to be the recommended working image. Does anybody have any clue on what might be going on? Thanks in advance. F.

4 7

Upload files from filesystem paths...
by Neil.Burdett＠csiro.au 10 Dec '12

10 Dec '12

Hi, I have a local galaxy installation. I've created a data library, selected "Upload files from filesystem paths", pasted a path in the "path to upload" window, and I've selected to preserve the directory structure". And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil

1 0

Exporting Trackster visualizations.
by Mohammad Heydarian 10 Dec '12

10 Dec '12

Hi, Is there a way to export visualizations from Trackster and Sweepster in .pdf or .jpg format? I have been using these fantastic tools to fine tune my parameters and would like to show how I did so in figure format (partially to locally get the word out about these powerful tools). Screenshots often do not suffice (and don't do the tools justice). Any solutions and/or fixes are appreciated! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205

2 1

About the output
by Chenhao 10 Dec '12

10 Dec '12

I made a galaxy tool which is just create a txt file. When I use this tool , I wish to let it show the detail of the txt. In the xml file I use : <output> <data name="test" format="txt"><output/> But it does not work, when I click the "eye" button in galaxy, a download dialog appear, but it is just a empty file. Could somebody tell me what should I do , I want show the txt detail in the galaxy.

1 0

add new slurm-drmaa runner to galaxy-central
by Di Pe 10 Dec '12

10 Dec '12

may be some other people would find this a useful enhancement: https://bitbucket.org/galaxy/galaxy-central/issue/778/add-new-slurm-drmaa-r…

2 1

Toolshed confusion
by greg 10 Dec '12

10 Dec '12

Hi guys, I have my fresh galaxy install on our cluster and now I'm trying to figure out which tools are missing and how to install them. I just came across the toolshed so now I'm really confused. Question 1: Can I install EVERY tool I need from the tool shed or are there some things I need to install manually first like R, Samtools, etc? How do I know what to install from where? Question 2: Is it preferable to use the toolshed whenever possible, or it is not fully developed yet? Thanks, Greg

2 3

Fix for SelectToolParameter rerun, workflow when multiple="true"
by Jim Johnson 10 Dec '12

10 Dec '12

Fix for SelectToolParameter rerun,workflow when multiple="true" The following change allows multiple select values to be set on rerun and in workflows. I checked that DrillDownSelectToolParameter and ColumnListParameter stiil worked. $ hg diff lib/galaxy/tools/parameters/basic.py diff -r 0042b30216fc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Nov 06 11:14:22 2012 -0800 +++ b/lib/galaxy/tools/parameters/basic.py Mon Dec 10 11:03:10 2012 -0600 @@ -715,6 +715,12 @@ if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value + def to_html_value( self, value, app ): + if isinstance( value, list ): + return value + else: + return str( value ) + def to_param_dict_string( self, value, other_values={} ): if value is None: return "None" Need to override method to_html_value() from ToolParameter otherwise a list value will be returned as a string: "['a','b']" instead of a list: ['a','b'] and options will not be selected in method get_html_field() : def get_html_field( self, trans=None, value=None, context={} ): # Dynamic options are not yet supported in workflow, allow # specifying the value as text for now. if self.need_late_validation( trans, context ): if value is not None: assert isinstance( value, UnvalidatedValue ), "Late validation needed for '%s', but provided value (%s) is not of type UnvalidatedValue (%s)." % ( self.name, value, type( value ) ) value = value.value if self.multiple: if value is None: value = "" else: value = "\n".join( value ) return form_builder.TextArea( self.name, value=value ) else: return form_builder.TextField( self.name, value=(value or "") ) if value is not None: if not isinstance( value, list ): value = [ value ] ### "['a','b']" is not a list so value set to ["['a','b']"] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: if isinstance( optval, UnvalidatedValue ): optval = optval.value text = "%s (unvalidated)" % text if value: selected = ( optval in value ) ### 'a' will not be found in: ["['a','b']"] field.add_option( text, optval, selected ) return field

2 1

Re: [galaxy-dev] postgres connection
by Coldren, Christopher D 10 Dec '12

10 Dec '12

That worked perfectly! Thanks Nate! Chris >> Galaxy dev: >> >> I'm installing a local galaxy instance (Dec 4, 2012 vintage) and it is running well under mySQL, but I'm having trouble getting it to work with a postgres database. >> >> I've done the following to create the db and provide permissions: >> >> $ whoami >> galaxy >> $ createdb galaxy_prod4 >> $ psql galaxy_prod4 >> psql (8.4.13) >> Type "help" for help. >> galaxy_prod4=# CREATE ROLE galaxy_prod_role4 WITH PASSWORD 'milkweed'; >> CREATE ROLE >> galaxy_prod4=# GRANT ALL PRIVILEGES ON DATABASE galaxy_prod4 to galaxy_prod_role4; >> GRANT >> galaxy_prod4=# ALTER ROLE galaxy_prod_role4 LOGIN; >> ALTER ROLE >> galaxy_prod4=# \du >> List of roles >> Role name | Attributes | Member of >> -------------------+--------------+----------- >> galaxy | Superuser | {} >> : Create role >> : Create DB >> galaxy_prod_role | Cannot login | {} >> galaxy_prod_role4 | | {} >> mydb_role | Cannot login | {} >> mydb_user | | {} >> postgres | Superuser | {} >> : Create role >> : Create DB >> galaxy_prod4=# \l >> List of databases >> Name | Owner | Encoding | Collation | Ctype | Access privileges >> --------------+----------+----------+-------------+-------------+------------------------------ >> galaxy_prod3 | galaxy | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/galaxy >> : galaxy=CTc/galaxy >> : galaxy_prod_role=CTc/galaxy >> galaxy_prod4 | galaxy | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/galaxy >> : galaxy=CTc/galaxy >> : galaxy_prod_role4=CTc/galaxy >> postgres | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | >> template0 | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =c/postgres >> : postgres=CTc/postgres >> template1 | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =c/postgres >> : postgres=CTc/postgres >> (5 rows) >> >> >> Looks promising, right? >> >> My universe_wsgi.ini has the following entry: >> >> >> database_connection = postgres:///galaxy_prod_role4:milkweed@127.0.0.1:5432/galaxy_prod4 > > Hi Chris, > > You're a field off in your URL, try this: > > postgres://galaxy_prod_role4:milkweed@127.0.0.1:5432/galaxy_prod4 > > --nate > >> >> and started the application, but it failed with: >> >> OperationalError: (OperationalError) FATAL: database "galaxy_prod_role4:milkweed@127.0.0.1:5432/galaxy_prod4" does not exist >> >> commenting the database_connection line out allows galaxy to start, using mySQL I presume. Any ideas? This is my first time configuring something like this. >> >> Thank you! >> Chris >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > >

1 0