Re: [galaxy-dev] DustMasker tool for ncbi_blast_plus
On Fri, Feb 15, 2013 at 6:10 PM, Nicola Soranzo wrote: >Peter wrote: >> >> It seems to have confused the bitbucket page a little, but I have >> checked in your initial wrapper to my development repository (I >> use the tools branch): >> https://bitbucket.org/peterjc/galaxy-central/commits/2284d485e36f74f19b0dbe78709b098d9eba4ef6 >> >> Note I'm not going to include this in the Tool Shed release yet, >> we need to sort out the file format definitions first. > > > Hi Peter, > I implemented minimal datatypes for maskinfo ASN.1 binary and text, plus > some other improvements to ncbi_blast_plus, and I sent you a pull > request through Bitbucket for your development repository. I think that > would be easier for you, let me know if it is not. > > Nicola > That looks very useful Nicola - I hope to have time to test that next week :) Thank you, Peter ___ 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/
Re: [galaxy-dev] DustMasker tool for ncbi_blast_plus
Il giorno lun, 11/02/2013 alle 13.19 +, Peter Cock ha scritto: > On Fri, Feb 8, 2013 at 4:30 PM, Nicola Soranzo wrote: > > Il giorno mer, 06/02/2013 alle 20.01 +0100, Nicola Soranzo ha scritto: > >> Hi Peter, > >> I added these file formats mostly as placeholders for a future > >> implementation. Now I have changed a bit the tool by removing acclist > >> and seqloc_xml formats since they are not recognized by the last > >> versions of dustmasker (I also sent an email to > >> blast-h...@ncbi.nlm.nih.gov to inform them of this bug). > >> As before, you can find the new version at: > >> > >> https://bitbucket.org/nsoranzo/ncbi_blast_plus > >> > >> I stripped the old commit and did a new one, not a very good practice, > >> sorry about that. > > It seems to have confused the bitbucket page a little, but I have > checked in your initial wrapper to my development repository (I > use the tools branch): > https://bitbucket.org/peterjc/galaxy-central/commits/2284d485e36f74f19b0dbe78709b098d9eba4ef6 > > Note I'm not going to include this in the Tool Shed release yet, > we need to sort out the file format definitions first. Hi Peter, I implemented minimal datatypes for maskinfo ASN.1 binary and text, plus some other improvements to ncbi_blast_plus, and I sent you a pull request through Bitbucket for your development repository. I think that would be easier for you, let me know if it is not. Nicola ___ 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/
Re: [galaxy-dev] New release : display problem
On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker wrote:
> Well, (un)fortunately this file works for me in both firefox and
> chrome on the current galaxy-dist. Just to confirm -- when you click
> the eye, it doesn't download the file either, right -- nothing at all
> happens?
>
> In chrome, could you open the console (Tools -> Javascript Console or
> Ctrl+Shift+J) and then try again, letting me know if there are any
> errors that show up?
>
This is the error I see in Chrome Javascript Console:
"Uncaught TypeError: undefined is not a function"
And this is the code around the line causing the error:
// Set up dataset and attributes.
var dataset = new data.TabularDataset( {"misc_blurb": "8,024 lines",
"name": "Join two Datasets on data 28 and data 36", "data_type":
"tabular", "metadata_columns": 5, "deleted": false,
"metadata_data_lines": 8024, "metadata_column_names": null,
"genome_build": "build37.2", "purged": false, "visible": true,
"state": "ok", "metadata_comment_lines": null, "file_size": 1569994,
"model_class": "HistoryDatasetAssociation", "metadata_column_types":
["str", "float", "list", "str", "int"], "id": 110, "misc_info": "",
"metadata_dbkey": "build37.2"} );
dataset.set('chunk_url',
"/datasets/f30a35c999095ed7/display");
Please let me know if there is something else I can do to help solve this issue.
Regards,
Carlos
___
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Re: [galaxy-dev] environment variables and paths for toolshed tools
On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster wrote: > > On Feb 15, 2013, at 11:45 AM, Peter Cock wrote: >> Actually for the example I am working on, the motif.py script would be >> the tool executable, called from motif.xml like this: >> >> motif.py $fasta_file $tabular_file >> >> i.e. A completely self contained Galaxy tool consisting of four files: >> >> motif.xml - Galaxy tool definition >> motif.txt - README file >> motif.py - Python script which is the tool >> motif.dat - Data file used by the Python script >> >> I am hoping that no further XML configuration files are needed in >> order to handle the data file. >> >> Peter > > In this case, your motif.xml file can be configured with the following: > > > motif.py $fasta_file $tabular_file > > > MOTIF_DAT_PATH > > > and your repository will need to include the following tool_dependencies.xml > file: > > > > > action="set_to">$REPOSITORY_INSTALL_DIR > > > That seems overly complicated. Would I not be able to assume that the motif.xml, motif.py, motif.dat etc are all in the same folder (then I can just use a relative path to find the data file - nice and easy). If not, how about simply defining $REPOSITORY_INSTALL_DIR within the XML language so I can do this: motif.py $fasta_file $tabular_file $REPOSITORY_INSTALL_DIR/motif.dat And/or defining $REPOSITORY_INSTALL_DIR as an environment variable which I can then use in the script (be it Python, Perl, shell, etc)? Thanks, Peter ___ 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/
Re: [galaxy-dev] environment variables and paths for toolshed tools
On Feb 15, 2013, at 11:45 AM, Peter Cock wrote: > On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster wrote: > > Usecase: Tool comes with a simple datafile (e.g. defining a search motif, > say motif.dat) which is used by a script (say motif.py) via a normal > Galaxy tool XML file (say motif.xml). > > Perhaps I can just put my data file next to the script and XML file, in > which case it is easy for the script to locate? But I assumed that > Galaxy best practice would be to use the tool-data folder somehow... > > Thanks, > > Peter >>> >>> Is there a documented example I should be reading? In this use case >>> (without any explicit XML markup), can I assume/have the motif.dat >>> file be installed in the same folder next to the motif.py script and tool >>> defining motif.xml file? >> >> This scenario uses a tool dependency that is included in the repository >> which is discussed in the following section of the tool shed wiki. Using >> this approach a tool config (Cheetah template) would have to be >> configured with the proper tag set and an associated >> tag set that would ultimately have the path to the motif.py >> script and motif.dat file defined in the environment. Of course, this >> assumes the motify.py script is not the tool executable itself. > > Actually for the example I am working on, the motif.py script would be > the tool executable, called from motif.xml like this: > > motif.py $fasta_file $tabular_file > > i.e. A completely self contained Galaxy tool consisting of four files: > > motif.xml - Galaxy tool definition > motif.txt - README file > motif.py - Python script which is the tool > motif.dat - Data file used by the Python script > > I am hoping that no further XML configuration files are needed in > order to handle the data file. > > Peter In this case, your motif.xml file can be configured with the following: motif.py $fasta_file $tabular_file MOTIF_DAT_PATH and your repository will need to include the following tool_dependencies.xml file: $REPOSITORY_INSTALL_DIR ___ 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/
Re: [galaxy-dev] Install NGSRich in local galaxy
Thank you Greg, I will contact the owner of that software and see if we can get it installed. Regards From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Friday, February 15, 2013 10:13 AM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] Install NGSRich in local galaxy Hello Hakeem, When searching the tool shed from Galaxy, only repositories that are automatically installable into Galaxy will be located. Repositories are considered "installable" if they contain valid Galaxy utilities (tools, proprietary datatypes, repository dependency definitions, tool dependency definitions ) that can be loaded and used within Galaxy. Since the ngsrich repository in the main Galaxy tool shed consists of only a README file ( not valid Galaxy utilities ), it was not displayed when you searched the tool shed from Galaxy. As you discovered, manually downloading the tar archive of the repository from the tool shed and attempting to get any of it's contents to display in Galaxy will not work either because it contains no useful Galaxy utilities. You may contact the repository owner to see if they are planning to add any valid Galaxy utilities in the near future. Greg Von Kuster On Feb 15, 2013, at 10:26 AM, Hakeem Almabrazi wrote: Thank you Greg, That what I tried to do initially but I could not find this tool the tool shed repository. Here is what I did, as an admin I went to Search and browse shed tool->Galaxy main tool shed Then I searched for "ngsrich" I could not find it. Then I looked under static category I still could not find it. I even went to the search page I looked for the software and still will not show up. I finally downloaded it manually but had not gone that far. I am not sure if what I did make sense or not or the right way to do. Can you please tell me how to find that tool other than what I did above? Or if what I did is missing something? I appreciate your help... From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, February 14, 2013 5:29 PM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] Install NGSRich in local galaxy Hello Hakeem, Here is a link to the tool shed wiki sections that provide all of the details for installing repositories from the tool shed into your local Galaxy instance. http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance We advise that you use the automatic installation process when installing into your Galaxy instance and not the manual installation process. Greg Von Kuster On Feb 14, 2013, at 5:48 PM, Hakeem Almabrazi wrote: HI, Does anyone know who to install NGSRich software on a local instance of Galaxy? I tried to install it from the shed_tool but it does not show up in the repository, so I manually downloaded it from http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=ngs&id=feaea37bb0f3bdca But now, I am not sure how to add it into my galaxy env. Any help will be highly appreciated ... Regards, ___ 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/ ___ 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/
Re: [galaxy-dev] environment variables and paths for toolshed tools
On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster wrote: Usecase: Tool comes with a simple datafile (e.g. defining a search motif, say motif.dat) which is used by a script (say motif.py) via a normal Galaxy tool XML file (say motif.xml). Perhaps I can just put my data file next to the script and XML file, in which case it is easy for the script to locate? But I assumed that Galaxy best practice would be to use the tool-data folder somehow... Thanks, Peter >> >> Is there a documented example I should be reading? In this use case >> (without any explicit XML markup), can I assume/have the motif.dat >> file be installed in the same folder next to the motif.py script and tool >> defining motif.xml file? > > This scenario uses a tool dependency that is included in the repository > which is discussed in the following section of the tool shed wiki. Using > this approach a tool config (Cheetah template) would have to be > configured with the proper tag set and an associated > tag set that would ultimately have the path to the motif.py > script and motif.dat file defined in the environment. Of course, this > assumes the motify.py script is not the tool executable itself. Actually for the example I am working on, the motif.py script would be the tool executable, called from motif.xml like this: motif.py $fasta_file $tabular_file i.e. A completely self contained Galaxy tool consisting of four files: motif.xml - Galaxy tool definition motif.txt - README file motif.py - Python script which is the tool motif.dat - Data file used by the Python script I am hoping that no further XML configuration files are needed in order to handle the data file. Peter ___ 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/
Re: [galaxy-dev] environment variables and paths for toolshed tools
Hi Peter, On Feb 15, 2013, at 11:14 AM, Peter Cock wrote: > On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster wrote: >>> >>> Hi guys, >>> >>> Reading the rest of the thread from December, Greg's new code did >>> get checked in and should be working (I've not tried this yet). >>> >>> However, I can't help feeling that defining the two environment variables >>> David suggested, $GALAXY_DATA_INDEX_DIR and/or $GALAXY_HOME, >>> would cover the majority of use cases and be far simpler for tool authors >>> to use. Am I overlooking something? >>> >>> Usecase: Tool comes with a simple datafile (e.g. defining a search motif, >>> say motif.dat) which is used by a script (say motif.py) via a normal >>> Galaxy tool XML file (say motif.xml). >>> >>> Perhaps I can just put my data file next to the script and XML file, in >>> which case it is easy for the script to locate? But I assumed that >>> Galaxy best practice would be to use the tool-data folder somehow... >>> >>> Thanks, >>> >>> Peter >> >> The current implementation places your motif.dat data file in the >> repository installation directory, and tools that are properly configured >> to locate dependencies that are included in the repository contents >> will find it. This approach allows for tool dependency discovery and >> easy maintenance when uninstalling repositories as all contents are >> kept where they were installed. Tools that are properly configured >> with tags will find dependencies because the >> associated env.sh file is sourced, providing the location of all >> dependencies to the environment. > > Is there a documented example I should be reading? In this use case > (without any explicit XML markup), can I assume/have the motif.dat > file be installed in the same folder next to the motif.py script and tool > defining motif.xml file? This scenario uses a tool dependency that is included in the repository which is discussed in the following section of the tool shed wiki. Using this approach a tool config (Cheetah template) would have to be configured with the proper tag set and an associated tag set that would ultimately have the path to the motif.py script and motif.dat file defined in the environment. Of course, this assumes the motify.py script is not the tool executable itself. http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time > >> If your motif.dat file is one that would be manually altered by the >> Galaxy administrator over time, perhaps automatically moving it >> to the GALAXY_DATA_INDEX_DIR is justified. However, in this >> case, uninstalling the repository would probably not uninstall the >> motif.dat file. Does this fit with what you are thinking? > > In this case no, I would not expect the motif.dat file to be edited. > > Does this mean GALAXY_DATA_INDEX_DIR and the galaxy > tool-data folder are intended for 'configuration' files the local admin > may need to edit, rather than static tool specific data file? Not necessarily, but with the exception of sample .loc files included in the repository, repository contents should not generally be required to be moved outside of their installation directory. > >> What kinds of files would require knowledge of the GALAXY_HOME >> directory? > > Knowing GALAXY_DATA_INDEX_DIR would probably cover most > cases, so knowing GALAXY_HOME is probably not needed. I believe that the current implementation supports locating all tool dependencies, whether included in the repository or 3-rd party, so I'm not sure introducing GALAXY_DATA_INDEX_DIR to the repository installation process will be beneficial. I can be swayed, however, if I see justification for supporting it. > > Regards, > > Peter > ___ > 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/ ___ 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/
Re: [galaxy-dev] Problems with rsync from datacache.g2.bx.psu.edu/indexes
On Feb 15, 2013, at 11:12 AM, Rodolfo Aramayo wrote: > Hi, > > I hope this is the right place to ask, > > I am trying to rsync from: > > rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ > > and I am getting the error: > > @ERROR: chroot failed > rsync error: error starting client-server protocol (code 5) at main.c(1534) > [Receiver=3.0.9 > > I know I can rsync to any other places > > Do you happen to know what is going on? Hi Rodolfo, The array on which the data cache is located is currently down due to an upgrade problem. We hope to have this fixed today. Sorry for the inconvenience. --nate > > Thanks > > --Rodolfo > > ___ > 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/ ___ 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/
Re: [galaxy-dev] Confusion on Updating Code
On Feb 15, 2013, at 11:13 AM, greg wrote: > Thanks! One followup, see below. > > -Greg > > On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor wrote: >> On Feb 15, 2013, at 10:45 AM, greg wrote: >> >> >> Migrate: >> >> % sh manage_db.sh upgrade >> >> Pay attention to whatever the first revision you are migrating from is. >> Probably 109 if you were at the 1/13 release. > > Where would the "109" come from? How would I find my number? Prior to running the database upgrade, you can use the `version` subcommand to determine your current database version: % sh manage_db.sh version 109 > >> >> If you need to downgrade: >> >> % sh manage_db.sh downgrade >> % rm lib/galaxy/model/migrate/versions/*.pyc >> % hg update > > What would I use for ? 109 in my example, it might be different for you if you're running an older version of Galaxy. --nate ___ 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/
Re: [galaxy-dev] environment variables and paths for toolshed tools
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster wrote: >> >> Hi guys, >> >> Reading the rest of the thread from December, Greg's new code did >> get checked in and should be working (I've not tried this yet). >> >> However, I can't help feeling that defining the two environment variables >> David suggested, $GALAXY_DATA_INDEX_DIR and/or $GALAXY_HOME, >> would cover the majority of use cases and be far simpler for tool authors >> to use. Am I overlooking something? >> >> Usecase: Tool comes with a simple datafile (e.g. defining a search motif, >> say motif.dat) which is used by a script (say motif.py) via a normal >> Galaxy tool XML file (say motif.xml). >> >> Perhaps I can just put my data file next to the script and XML file, in >> which case it is easy for the script to locate? But I assumed that >> Galaxy best practice would be to use the tool-data folder somehow... >> >> Thanks, >> >> Peter > > The current implementation places your motif.dat data file in the > repository installation directory, and tools that are properly configured > to locate dependencies that are included in the repository contents > will find it. This approach allows for tool dependency discovery and > easy maintenance when uninstalling repositories as all contents are > kept where they were installed. Tools that are properly configured > with tags will find dependencies because the > associated env.sh file is sourced, providing the location of all > dependencies to the environment. Is there a documented example I should be reading? In this use case (without any explicit XML markup), can I assume/have the motif.dat file be installed in the same folder next to the motif.py script and tool defining motif.xml file? > If your motif.dat file is one that would be manually altered by the > Galaxy administrator over time, perhaps automatically moving it > to the GALAXY_DATA_INDEX_DIR is justified. However, in this > case, uninstalling the repository would probably not uninstall the > motif.dat file. Does this fit with what you are thinking? In this case no, I would not expect the motif.dat file to be edited. Does this mean GALAXY_DATA_INDEX_DIR and the galaxy tool-data folder are intended for 'configuration' files the local admin may need to edit, rather than static tool specific data file? > What kinds of files would require knowledge of the GALAXY_HOME > directory? Knowing GALAXY_DATA_INDEX_DIR would probably cover most cases, so knowing GALAXY_HOME is probably not needed. Regards, Peter ___ 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/
[galaxy-dev] Problems with rsync from datacache.g2.bx.psu.edu/indexes
Hi, I hope this is the right place to ask, I am trying to rsync from: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ and I am getting the error: @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1534) [Receiver=3.0.9 I know I can rsync to any other places Do you happen to know what is going on? Thanks --Rodolfo ___ 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/
Re: [galaxy-dev] Confusion on Updating Code
Thanks! One followup, see below. -Greg On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor wrote: > On Feb 15, 2013, at 10:45 AM, greg wrote: > > > Migrate: > > % sh manage_db.sh upgrade > > Pay attention to whatever the first revision you are migrating from is. > Probably 109 if you were at the 1/13 release. Where would the "109" come from? How would I find my number? > > If you need to downgrade: > > % sh manage_db.sh downgrade > % rm lib/galaxy/model/migrate/versions/*.pyc > % hg update What would I use for ? ___ 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/
Re: [galaxy-dev] Install NGSRich in local galaxy
Hello Hakeem, When searching the tool shed from Galaxy, only repositories that are automatically installable into Galaxy will be located. Repositories are considered "installable" if they contain valid Galaxy utilities (tools, proprietary datatypes, repository dependency definitions, tool dependency definitions ) that can be loaded and used within Galaxy. Since the ngsrich repository in the main Galaxy tool shed consists of only a README file ( not valid Galaxy utilities ), it was not displayed when you searched the tool shed from Galaxy. As you discovered, manually downloading the tar archive of the repository from the tool shed and attempting to get any of it's contents to display in Galaxy will not work either because it contains no useful Galaxy utilities. You may contact the repository owner to see if they are planning to add any valid Galaxy utilities in the near future. Greg Von Kuster On Feb 15, 2013, at 10:26 AM, Hakeem Almabrazi wrote: > Thank you Greg, > > That what I tried to do initially but I could not find this tool the tool > shed repository. Here is what I did, as an admin I went to Search and browse > shed tool->Galaxy main tool shed > Then I searched for “ngsrich” I could not find it. Then I looked under > static category I still could not find it. I even went to the search page I > looked for the software and still will not show up. I finally downloaded it > manually but had not gone that far. > > I am not sure if what I did make sense or not or the right way to do. Can > you please tell me how to find that tool other than what I did above? Or if > what I did is missing something? > > I appreciate your help… > > > > From: Greg Von Kuster [mailto:g...@bx.psu.edu] > Sent: Thursday, February 14, 2013 5:29 PM > To: Hakeem Almabrazi > Cc: Galaxy Dev > Subject: Re: [galaxy-dev] Install NGSRich in local galaxy > > Hello Hakeem, > > Here is a link to the tool shed wiki sections that provide all of the details > for installing repositories from the tool shed into your local Galaxy > instance. > > http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance > > We advise that you use the automatic installation process when installing > into your Galaxy instance and not the manual installation process. > > Greg Von Kuster > > > On Feb 14, 2013, at 5:48 PM, Hakeem Almabrazi wrote: > > > HI, > > Does anyone know who to install NGSRich software on a local instance of > Galaxy? > > I tried to install it from the shed_tool but it does not show up in the > repository, so I manually downloaded it from > http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=ngs&id=feaea37bb0f3bdca > > But now, I am not sure how to add it into my galaxy env. > > Any help will be highly appreciated … > > Regards, > > > > > > ___ > 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/ > ___ 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/
Re: [galaxy-dev] New release : display problem
Well, (un)fortunately this file works for me in both firefox and chrome on the current galaxy-dist. Just to confirm -- when you click the eye, it doesn't download the file either, right -- nothing at all happens? In chrome, could you open the console (Tools -> Javascript Console or Ctrl+Shift+J) and then try again, letting me know if there are any errors that show up? On Fri, Feb 15, 2013 at 3:32 AM, Mathieu Bahin wrote: > Hi, > > Enclosed is a dataset that I am not able to see anymore. > I don't see any error in the log (but maybe I missed it !). > > To answer to Carlos, I have the problem with Firefox and Chrome. > > Cheers, > Mathieu > > - Mail original - >> De: "Dannon Baker" >> À: "Mathieu Bahin" >> Cc: galaxy-dev@lists.bx.psu.edu >> Envoyé: Jeudi 14 Février 2013 17:01:02 >> Objet: Re: [galaxy-dev] New release : display problem >> >> Could you share with me a file that reproduces this behavior? I'm >> unable to do so on a fresh -dist clone after trying various files and >> file types. >> >> Do you see any errors in the console or galaxy log when this happens? >> >> >> On Thu, Feb 14, 2013 at 2:34 AM, Mathieu Bahin >> wrote: >> > Hi, >> > >> > Thanks for the answer. >> > >> > It is after the new galaxy-dist release and if a type is affected, >> > all its >> > children types are too. For example the tabular but that's not the >> > only one. >> > It's is not a question of size I think because very small datasets >> > are not >> > displayed neither. >> > >> > Cheers, >> > Mathieu >> > >> > >> > >> > De: "Dannon Baker" >> > À: "Mathieu Bahin" >> > Cc: galaxy-dev@lists.bx.psu.edu >> > Envoyé: Jeudi 14 Février 2013 00:55:46 >> > Objet: Re: [galaxy-dev] New release : display problem >> > >> > >> > Mathieu, >> > >> > To clarify -- is this after the new galaxy-dist release, or new >> > code in >> > galaxy-central? And, is this *any* tabular file? Or just ones of >> > a >> > particular size? (Files of > 50 columns are handled as a special >> > case, for >> > instance) >> > >> > -Dannon >> > >> > On Wed, Feb 13, 2013 at 11:29 AM, Mathieu Bahin >> > >> > wrote: >> >> >> >> Hi there, >> >> >> >> I am using my own Galaxy instance and since I updated, I can't see >> >> file of >> >> several datatypes (for example the 'tabular') clicking on the eye >> >> icon. >> >> >> >> Is that a problem linked to the new release ? >> >> >> >> Cheers, >> >> Mathieu Bahin >> >> >> >> ___ >> >> 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/ >> > >> > >> > >> ___ 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/
Re: [galaxy-dev] environment variables and paths for toolshed tools
Hello Peter, please see my response at the end.
On Feb 15, 2013, at 6:47 AM, Peter Cock wrote:
>>> On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
>>>
>>> Are there any environment variables that are honored by toolshed installed
>>> tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
>>> $GALAXY_HOME, then uploaded it the test toolshed, then installed it
>>> automatically. Neither of these resolved to what I expected. I don't want
>>> to hard-code the path in the xml tool file, but rather have a default
>>> location for other executables and jar files. How should this best be done?
>>>
>>> David Hoover
>>> Helix Systems Staff
>
> On Wed, Sep 12, 2012 at 6:15 PM, Greg Von Kuster wrote:
>> Hello David,
>>
>> This is not currently possible, but will be available in the next Galaxy
>> distribution release, currently scheduled for about 10 days from now. You
>> will include a tool_dependencies.xml file in your tool shed repository that
>> looks something like the following.
>>
>>
>>
>>
>>> action="set_to">$INSTALL_DIR
>>
>>
>>
>> Your tool will find the required files via the defined JAVA_JAR_PATH by
>> using a tag set in the tool config, something like this:
>>
>>
>>JAVA_JAR_PATH
>>
>>
>> The tag in the tool config would be something like this:
>>
>>
>> python_wrapper.py $JAVA_JAR_PATH/some_file.jar $param1 $param2...
>>
>>
>> I'm close to having this working, so if you are interested in testing before
>> the next Galaxy dist release, let me know and I'll tell you when the Galaxy
>> central repository has the new feature.
>>
>> Thanks!
>>
>> Greg Von Kuster
>
> Hi guys,
>
> Reading the rest of the thread from December, Greg's new code did
> get checked in and should be working (I've not tried this yet).
>
> However, I can't help feeling that defining the two environment variables
> David suggested, $GALAXY_DATA_INDEX_DIR and/or $GALAXY_HOME,
> would cover the majority of use cases and be far simpler for tool authors
> to use. Am I overlooking something?
>
> Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
> say motif.dat) which is used by a script (say motif.py) via a normal
> Galaxy tool XML file (say motif.xml).
>
> Perhaps I can just put my data file next to the script and XML file, in
> which case it is easy for the script to locate? But I assumed that
> Galaxy best practice would be to use the tool-data folder somehow...
>
> Thanks,
>
> Peter
The current implementation places your motif.dat data file in the repository
installation directory, and tools that are properly configured to locate
dependencies that are included in the repository contents will find it. This
approach allows for tool dependency discovery and easy maintenance when
uninstalling repositories as all contents are kept where they were installed.
Tools that are properly configured with tags will find
dependencies because the associated env.sh file is sourced, providing the
location of all dependencies to the environment.
If your motif.dat file is one that would be manually altered by the Galaxy
administrator over time, perhaps automatically moving it to the
GALAXY_DATA_INDEX_DIR is justified. However, in this case, uninstalling the
repository would probably not uninstall the motif.dat file. Does this fit with
what you are thinking?
What kinds of files would require knowledge of the GALAXY_HOME directory?
Thanks Peter,
Greg Von Kuster
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Re: [galaxy-dev] Confusion on Updating Code
On Feb 15, 2013, at 10:45 AM, greg wrote: > Hi guys, > > I'm trying to do my first update on my local galaxy install (it's been > a few months at least since I installed) > > I'm trying to follow the instructions here to update the code: > http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date > > My first question is how do I roll back if something goes wrong in the > upgrade? Hi Greg, Collect your current changeset with: % hg parents changeset: 8563:a4113cc1cb5e tag: release_2013.01.13 parent: 8529:ce62bf5a91f8 user:Daniel Blankenberg date:Thu Jan 10 14:57:37 2013 -0500 summary: Fixes for Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes an issue where rurun would select the wrong input dataset. Update: % hg pull % hg update release_2013.02.08 Migrate: % sh manage_db.sh upgrade Pay attention to whatever the first revision you are migrating from is. Probably 109 if you were at the 1/13 release. If you need to downgrade: % sh manage_db.sh downgrade % rm lib/galaxy/model/migrate/versions/*.pyc % hg update > My second question is that this page > http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08 says that I > need to do something to get onto the stable branch? Right now when I > run hg branch it says default. I'd prefer to be on stable. Any idea > what I should do? (and again how can I roll back to the code i have > now if something goes wrong?) The stable branch is new, so your old clone won't have it until you pull new changesets. As long as you do `hg pull` rather than `hg pull -u` and then explicitly update to the release tag or stable branch (`hg update release_2013.02.08` or `hg update stable`), you'll be on the stable branch. --nate > > Thanks, > > Greg > > Summary information: > > [galaxy@vm244]/usr/local/galaxy/galaxy-dist>hg summary > parent: 7986:12fcd068b12e tip > Do not hide failed datasets with HideDatasetAction post job action. > branch: default > commit: 3721 modified, 9 unknown > update: (current) > ___ > 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/ ___ 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/
Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed
It's really hard to say what's going on with those issues without more
information about the particular version of galaxy (which
unfortunately we'd get from `hg tip`, which won't work on your bio
linux install) or proxy configuration, if any. I'm also not sure what
the appropriate bio linux update procedure is or how much
customization they've done to galaxy to make all the tools work in
that environment, but what I'd personally try would be to just clone a
fresh galaxy (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) and
migrate your configuration files, etc. if you find that it works.
Once you have an actual mercurial repository updates are trivial (just
the `hg pull -u` that you already tried).
-Dannon
On Thu, Feb 14, 2013 at 2:08 PM, David Joly wrote:
> I still haven't heard back from the Bio-Linux guys regarding how to update
> Galaxy within Bio-Linux...
>
> In the meantime, I tried to play with the "Manage data libraries", in order
> to import large datasets. I modified the "library_import_dir" line in the
> universe_wsgi.ini. The first thing I can say is that when you make a mistake
> in the path (e.g. "../../directory" instead of "../../../directory"), Galaxy
> won't start at all! Anyway, even now that I figured that out, "This dataset
> is uploading" stays forever. As a test, I tried to upload small dataset
> using the usual way ("Get Data"), and here too "Dataset is uploading" stays
> forever. If I revert the "library_import_dir" to normal, I can upload via
> "Get Data".
>
> Is this also an issue related to the Galaxy version I'm using? Or is the
> Galaxy in Bio-Linux screwed up?
>
> Many thanks,
>
> DJ
>
>
> 2013/2/13 David Joly
>>
>> This could be the problem, I just installed BioLinux 7 on my computer with
>> Galaxy running out-of-the-box...
>>
>> However, it looks like they changed a few things, there is no .hg file and
>> no galaxy-dist folder. Can I update outside of mercurial?
>>
>>
>> 2013/2/13 Dannon Baker
>>>
>>> How old is the galaxy you're running? To use the main toolshed you'll
>>> need to use a galaxy-dist release from December or later. After this point
>>> in time the interface was standardized and is backwards compatible.
>>>
>>> To update, you should be able to simply navigate to your galaxy-dist
>>> directory, 'hg pull -u', and you'll be off and running.
>>>
>>> Also, since this deals with a local install, please do keep replies on
>>> the 'galaxy-dev' list that I transitioned this thread to instead of
>>> galaxy-user.
>>>
>>> Thanks!
>>>
>>> -Dannon
>>>
>>> On Feb 13, 2013, at 6:43 PM, David Joly wrote:
>>>
>>> > Ok, one more step closer (I thought closing the browser would be enough
>>> > to restart galaxy, but obviously, I had to reboot the computer).
>>> >
>>> > But now it says: ValueError: too many values to unpack
>>> >
>>> >
>>> > 2013/2/13 Dannon Baker
>>> > On Feb 13, 2013, at 6:16 PM, David Joly wrote:
>>> >
>>> > > Hi!
>>> > >
>>> > > Ok, I know many people had the same issue, but I just can't figure
>>> > > what's going on. I'm quite new about using a local instance of Galaxy
>>> > > and
>>> > > I'm trying to figure how to install a tool from the tool shed. Reading
>>> > > the
>>> > > tutorial (Installing Galaxy tool shed repository tools into a local
>>> > > Galaxy
>>> > > instance) looked pretty simple, but maybe I missed something.
>>> > >
>>> > > First, I modified the universe_wsgi.ini file by removing the "#"
>>> > > before the tool_config_file and tool_path lines.
>>> >
>>> > This one step should really be all you need to do (any other files get
>>> > created automatically with reasonable defaults if missing) as far as
>>> > configuration goes. Did you restart your galaxy instance after editing
>>> > universe_wsgi.ini?
>>> >
>>> > -Dannon
>>> >
>>>
>>
>
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[galaxy-dev] Confusion on Updating Code
Hi guys, I'm trying to do my first update on my local galaxy install (it's been a few months at least since I installed) I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date My first question is how do I roll back if something goes wrong in the upgrade? My second question is that this page http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08 says that I need to do something to get onto the stable branch? Right now when I run hg branch it says default. I'd prefer to be on stable. Any idea what I should do? (and again how can I roll back to the code i have now if something goes wrong?) Thanks, Greg Summary information: [galaxy@vm244]/usr/local/galaxy/galaxy-dist>hg summary parent: 7986:12fcd068b12e tip Do not hide failed datasets with HideDatasetAction post job action. branch: default commit: 3721 modified, 9 unknown update: (current) ___ 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/
Re: [galaxy-dev] Install NGSRich in local galaxy
Thank you Greg, That what I tried to do initially but I could not find this tool the tool shed repository. Here is what I did, as an admin I went to Search and browse shed tool->Galaxy main tool shed Then I searched for "ngsrich" I could not find it. Then I looked under static category I still could not find it. I even went to the search page I looked for the software and still will not show up. I finally downloaded it manually but had not gone that far. I am not sure if what I did make sense or not or the right way to do. Can you please tell me how to find that tool other than what I did above? Or if what I did is missing something? I appreciate your help... From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, February 14, 2013 5:29 PM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] Install NGSRich in local galaxy Hello Hakeem, Here is a link to the tool shed wiki sections that provide all of the details for installing repositories from the tool shed into your local Galaxy instance. http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance We advise that you use the automatic installation process when installing into your Galaxy instance and not the manual installation process. Greg Von Kuster On Feb 14, 2013, at 5:48 PM, Hakeem Almabrazi wrote: HI, Does anyone know who to install NGSRich software on a local instance of Galaxy? I tried to install it from the shed_tool but it does not show up in the repository, so I manually downloaded it from http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=ngs&id=feaea37bb0f3bdca But now, I am not sure how to add it into my galaxy env. Any help will be highly appreciated ... Regards, ___ 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/ ___ 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/
Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
Ok, I created a ~/.hgrc file and add this: [trusted] users=galaxy It seems to have fixed it. -Greg On Fri, Feb 15, 2013 at 9:50 AM, greg wrote: > Thanks. > > I'm trying to follow the instructions here to update the code: > http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date > > But I'm getting this error: > >>hg incoming > Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from > untrusted user galaxy, group scicomp > Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from > untrusted user galaxy, group scicomp > abort: repository default not found! > > -Greg > > On Fri, Feb 15, 2013 at 9:45 AM, Greg Von Kuster wrote: >> Hello Greg, >> >> What version of Galaxy are you running - it is likely older than the >> December 20, 2012 Galaxy release. You'll have to upgrade to at least that >> release to use the main Galaxy tool shed. >> >> Greg Von Kuster >> >> On Feb 15, 2013, at 9:43 AM, greg wrote: >> >>> Hi guys, >>> >>> I'm getting an error when trying to install this from the toolshed? >>> Let me know what I should do? >>> >>> Thanks, >>> >>> Greg >>> >>> Error - : too many values to unpack >>> URL: >>> http://galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=67abe7fe2882a54c&changeset_revisions=cdd9791c0afa >>> File >>> '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', >>> line 143 in __call__ >>> app_iter = self.application(environ, start_response) >>> File >>> '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', >>> line 80 in __call__ >>> return self.application(environ, start_response) >>> File >>> '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', >>> line 91 in __call__ >>> return self.app( environ, start_response ) >>> File >>> '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', >>> line 632 in __call__ >>> return self.application(environ, start_response) >>> File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >>> line 160 in __call__ >>> body = method( trans, **kwargs ) >>> File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', >>> line 206 in decorator >>> return func( self, trans, *args, **kwargs ) >>> File >>> '/misc/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >>> line 1201 in prepare_for_install >>> description, repository_clone_url, changeset_revision, ctx_rev, >>> repository_owner, tool_dependencies = repo_info_tuple >>> ValueError: too many values to unpack >>> >>> >>> >>> On Fri, Feb 15, 2013 at 9:39 AM, James Taylor wrote: You likely want the newest version (3) On Feb 15, 2013 9:37 AM, "greg" wrote: > > Thanks! So one question, when I go to install it from the toolshed I > see two choices for a revision to select: > > 3:cdd9791c0afa > 0:c1eeccec29d1 > > Which would I choose and why? > > Thanks, > > Greg > > On Fri, Feb 15, 2013 at 9:30 AM, James Taylor > wrote: >> The wrapper you are using is for MACS 1.3, there is a wrapper that is >> compatible with 1.4 in the toolshed. >> >> -- >> James Taylor, Assistant Professor, Biology/CS, Emory University >> >> >> On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: >>> Hi guys, >>> >>> I'm trying to run MACS in my local galaxy install (see screenshot: >>> http://snag.gy/5QGUH.jpg) >>> >>> And I'm getting this error: >>> >>> Usage: macs <-t tfile> [-n name] [-g genomesize] [options] >>> >>> Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w >>> --call-subpeaks >>> >>> macs: error: no such option: --lambdaset >>> >>> Thanks in advance for any help. >>> >>> -Greg >>> >>> Here's how I installed Macs (I guess it doesn't come built in?) >>> cd /usr/local/galaxy/downloads/ wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz tar -xzvf MACS-1.4.2-1.tar.gz cd MACS-1.4.2 source /usr/local/galaxy/job_environment_setup_file python setup.py install deactivate cd /misc/local/galaxy/galaxy_python/bin ln -s macs14 macs >>> >>> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy >>> user's path) >>> ___ >>> 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/ >>> ___ >>> 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:
Re: [galaxy-dev] New release : display problem
Hi, Enclosed is a dataset that I am not able to see anymore. I don't see any error in the log (but maybe I missed it !). To answer to Carlos, I have the problem with Firefox and Chrome. Cheers, Mathieu - Mail original - > De: "Dannon Baker" > À: "Mathieu Bahin" > Cc: galaxy-dev@lists.bx.psu.edu > Envoyé: Jeudi 14 Février 2013 17:01:02 > Objet: Re: [galaxy-dev] New release : display problem > > Could you share with me a file that reproduces this behavior? I'm > unable to do so on a fresh -dist clone after trying various files and > file types. > > Do you see any errors in the console or galaxy log when this happens? > > > On Thu, Feb 14, 2013 at 2:34 AM, Mathieu Bahin > wrote: > > Hi, > > > > Thanks for the answer. > > > > It is after the new galaxy-dist release and if a type is affected, > > all its > > children types are too. For example the tabular but that's not the > > only one. > > It's is not a question of size I think because very small datasets > > are not > > displayed neither. > > > > Cheers, > > Mathieu > > > > > > > > De: "Dannon Baker" > > À: "Mathieu Bahin" > > Cc: galaxy-dev@lists.bx.psu.edu > > Envoyé: Jeudi 14 Février 2013 00:55:46 > > Objet: Re: [galaxy-dev] New release : display problem > > > > > > Mathieu, > > > > To clarify -- is this after the new galaxy-dist release, or new > > code in > > galaxy-central? And, is this *any* tabular file? Or just ones of > > a > > particular size? (Files of > 50 columns are handled as a special > > case, for > > instance) > > > > -Dannon > > > > On Wed, Feb 13, 2013 at 11:29 AM, Mathieu Bahin > > > > wrote: > >> > >> Hi there, > >> > >> I am using my own Galaxy instance and since I updated, I can't see > >> file of > >> several datatypes (for example the 'tabular') clicking on the eye > >> icon. > >> > >> Is that a problem linked to the new release ? > >> > >> Cheers, > >> Mathieu Bahin > >> > >> ___ > >> 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/ > > > > > > > taxlevel rankID taxon daughterlevels total AM1_106m AM1_119m AM1_121m AM1_143m AM1_18m AM1_19 AM1_1m AM1_20m AM1_21m AM1_28 AM1_29 AM1_2m AM1_30m AM1_32m AM1_37m AM1_51m AM1_55 AM1_58 AM1_61 AM1_63m AM1_68m AM1_7 AM1_70m AM1_76m AM1_81m AM1_84m AM1_89m AM1_94m 0 0 Root 1 5 1 1 1 1 1 1 1 1 1 2 1 1 2 3 1 1 3 3 1 1 1 2 1 1 1 1 3 1 1 0.3 Eukaryota 2 5 1 1 1 1 1 1 1 1 1 2 1 1 2 3 1 1 3 3 1 1 1 2 1 1 1 1 3 1 2 0.3.15 Opisthokonta 1 3 0 1 1 0 1 0 1 1 0 2 1 0 1 2 1 0 3 3 1 1 1 1 0 1 1 1 1 1 3 0.3.15.1 Fungi 2 3 0 1 1 0 1 0 1 1 0 2 1 0 1 2 1 0 3 3 1 1 1 1 0 1 1 1 1 1 4 0.3.15.1.5 Fungi 1 2 0 0 0 0 1 0 1 0 0 1 0 0 0 2 0 0 2 2 1 1 1 1 0 1 1 1 1 1 5 0.3.15.1.5.1 Basal fungi 1 2 0 0 0 0 1 0 1 0 0 1 0 0 0 2 0 0 2 2 1 1 1 1 0 1 1 1 1 1 6 0.3.15.1.5.1.1 Basal fungi 1 2 0 0 0 0 1 0 1 0 0 1 0 0 0 2 0 0 2 2 1 1 1 1 0 1 1 1 1 1 4 0.3.15.1.10 unclassified 1 1 0 1 1 0 0 0 0 1 0 1 1 0 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 2 0.3.20 unclassified 1 2 1 0 0 1 0 1 0 0 1 0 0 1 1 1 0 1 0 0 0 0 0 1 1 0 0 0 2 0 ___ 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/
Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed
I still haven't heard back from the Bio-Linux guys regarding how to update
Galaxy within Bio-Linux...
In the meantime, I tried to play with the "Manage data libraries", in order
to import large datasets. I modified the "library_import_dir" line in the
universe_wsgi.ini. The first thing I can say is that when you make a
mistake in the path (e.g. "../../directory" instead of
"../../../directory"), Galaxy won't start at all! Anyway, even now that I
figured that out, "This dataset is uploading" stays forever. As a test, I
tried to upload small dataset using the usual way ("Get Data"), and here
too "Dataset is uploading" stays forever. If I revert the
"library_import_dir" to normal, I can upload via "Get Data".
Is this also an issue related to the Galaxy version I'm using? Or is the
Galaxy in Bio-Linux screwed up?
Many thanks,
DJ
2013/2/13 David Joly
> This could be the problem, I just installed BioLinux 7 on my computer with
> Galaxy running out-of-the-box...
>
> However, it looks like they changed a few things, there is no .hg file and
> no galaxy-dist folder. Can I update outside of mercurial?
>
>
> 2013/2/13 Dannon Baker
>
>> How old is the galaxy you're running? To use the main toolshed you'll
>> need to use a galaxy-dist release from December or later. After this point
>> in time the interface was standardized and is backwards compatible.
>>
>> To update, you should be able to simply navigate to your galaxy-dist
>> directory, 'hg pull -u', and you'll be off and running.
>>
>> Also, since this deals with a local install, please do keep replies on
>> the 'galaxy-dev' list that I transitioned this thread to instead of
>> galaxy-user.
>>
>> Thanks!
>>
>> -Dannon
>>
>> On Feb 13, 2013, at 6:43 PM, David Joly wrote:
>>
>> > Ok, one more step closer (I thought closing the browser would be enough
>> to restart galaxy, but obviously, I had to reboot the computer).
>> >
>> > But now it says: ValueError: too many values to unpack
>> >
>> >
>> > 2013/2/13 Dannon Baker
>> > On Feb 13, 2013, at 6:16 PM, David Joly wrote:
>> >
>> > > Hi!
>> > >
>> > > Ok, I know many people had the same issue, but I just can't figure
>> what's going on. I'm quite new about using a local instance of Galaxy and
>> I'm trying to figure how to install a tool from the tool shed. Reading the
>> tutorial (Installing Galaxy tool shed repository tools into a local Galaxy
>> instance) looked pretty simple, but maybe I missed something.
>> > >
>> > > First, I modified the universe_wsgi.ini file by removing the "#"
>> before the tool_config_file and tool_path lines.
>> >
>> > This one step should really be all you need to do (any other files get
>> created automatically with reasonable defaults if missing) as far as
>> configuration goes. Did you restart your galaxy instance after editing
>> universe_wsgi.ini?
>> >
>> > -Dannon
>> >
>>
>>
>
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Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
Thanks. I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date But I'm getting this error: >hg incoming Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp abort: repository default not found! -Greg On Fri, Feb 15, 2013 at 9:45 AM, Greg Von Kuster wrote: > Hello Greg, > > What version of Galaxy are you running - it is likely older than the December > 20, 2012 Galaxy release. You'll have to upgrade to at least that release to > use the main Galaxy tool shed. > > Greg Von Kuster > > On Feb 15, 2013, at 9:43 AM, greg wrote: > >> Hi guys, >> >> I'm getting an error when trying to install this from the toolshed? >> Let me know what I should do? >> >> Thanks, >> >> Greg >> >> Error - : too many values to unpack >> URL: >> http://galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=67abe7fe2882a54c&changeset_revisions=cdd9791c0afa >> File >> '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', >> line 143 in __call__ >> app_iter = self.application(environ, start_response) >> File >> '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', >> line 80 in __call__ >> return self.application(environ, start_response) >> File >> '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', >> line 91 in __call__ >> return self.app( environ, start_response ) >> File >> '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', >> line 632 in __call__ >> return self.application(environ, start_response) >> File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 160 in __call__ >> body = method( trans, **kwargs ) >> File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', >> line 206 in decorator >> return func( self, trans, *args, **kwargs ) >> File >> '/misc/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >> line 1201 in prepare_for_install >> description, repository_clone_url, changeset_revision, ctx_rev, >> repository_owner, tool_dependencies = repo_info_tuple >> ValueError: too many values to unpack >> >> >> >> On Fri, Feb 15, 2013 at 9:39 AM, James Taylor wrote: >>> You likely want the newest version (3) >>> >>> On Feb 15, 2013 9:37 AM, "greg" wrote: Thanks! So one question, when I go to install it from the toolshed I see two choices for a revision to select: 3:cdd9791c0afa 0:c1eeccec29d1 Which would I choose and why? Thanks, Greg On Fri, Feb 15, 2013 at 9:30 AM, James Taylor wrote: > The wrapper you are using is for MACS 1.3, there is a wrapper that is > compatible with 1.4 in the toolshed. > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: >> Hi guys, >> >> I'm trying to run MACS in my local galaxy install (see screenshot: >> http://snag.gy/5QGUH.jpg) >> >> And I'm getting this error: >> >> Usage: macs <-t tfile> [-n name] [-g genomesize] [options] >> >> Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w >> --call-subpeaks >> >> macs: error: no such option: --lambdaset >> >> Thanks in advance for any help. >> >> -Greg >> >> Here's how I installed Macs (I guess it doesn't come built in?) >> >>> cd /usr/local/galaxy/downloads/ >>> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz >>> tar -xzvf MACS-1.4.2-1.tar.gz >>> cd MACS-1.4.2 >>> source /usr/local/galaxy/job_environment_setup_file >>> python setup.py install >>> deactivate >>> cd /misc/local/galaxy/galaxy_python/bin >>> ln -s macs14 macs >> >> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy >> user's path) >> ___ >> 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/ >> ___ >> 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/ > ___ 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/
Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
Hello Greg, What version of Galaxy are you running - it is likely older than the December 20, 2012 Galaxy release. You'll have to upgrade to at least that release to use the main Galaxy tool shed. Greg Von Kuster On Feb 15, 2013, at 9:43 AM, greg wrote: > Hi guys, > > I'm getting an error when trying to install this from the toolshed? > Let me know what I should do? > > Thanks, > > Greg > > Error - : too many values to unpack > URL: > http://galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=67abe7fe2882a54c&changeset_revisions=cdd9791c0afa > File > '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File > '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', > line 91 in __call__ > return self.app( environ, start_response ) > File > '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', > line 206 in decorator > return func( self, trans, *args, **kwargs ) > File > '/misc/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', > line 1201 in prepare_for_install > description, repository_clone_url, changeset_revision, ctx_rev, > repository_owner, tool_dependencies = repo_info_tuple > ValueError: too many values to unpack > > > > On Fri, Feb 15, 2013 at 9:39 AM, James Taylor wrote: >> You likely want the newest version (3) >> >> On Feb 15, 2013 9:37 AM, "greg" wrote: >>> >>> Thanks! So one question, when I go to install it from the toolshed I >>> see two choices for a revision to select: >>> >>> 3:cdd9791c0afa >>> 0:c1eeccec29d1 >>> >>> Which would I choose and why? >>> >>> Thanks, >>> >>> Greg >>> >>> On Fri, Feb 15, 2013 at 9:30 AM, James Taylor >>> wrote: The wrapper you are using is for MACS 1.3, there is a wrapper that is compatible with 1.4 in the toolshed. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: > Hi guys, > > I'm trying to run MACS in my local galaxy install (see screenshot: > http://snag.gy/5QGUH.jpg) > > And I'm getting this error: > > Usage: macs <-t tfile> [-n name] [-g genomesize] [options] > > Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w > --call-subpeaks > > macs: error: no such option: --lambdaset > > Thanks in advance for any help. > > -Greg > > Here's how I installed Macs (I guess it doesn't come built in?) > >> cd /usr/local/galaxy/downloads/ >> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz >> tar -xzvf MACS-1.4.2-1.tar.gz >> cd MACS-1.4.2 >> source /usr/local/galaxy/job_environment_setup_file >> python setup.py install >> deactivate >> cd /misc/local/galaxy/galaxy_python/bin >> ln -s macs14 macs > > (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy > user's path) > ___ > 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/ > ___ > 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/ ___ 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/
Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
Hi guys, I'm getting an error when trying to install this from the toolshed? Let me know what I should do? Thanks, Greg Error - : too many values to unpack URL: http://galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=67abe7fe2882a54c&changeset_revisions=cdd9791c0afa File '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 206 in decorator return func( self, trans, *args, **kwargs ) File '/misc/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack On Fri, Feb 15, 2013 at 9:39 AM, James Taylor wrote: > You likely want the newest version (3) > > On Feb 15, 2013 9:37 AM, "greg" wrote: >> >> Thanks! So one question, when I go to install it from the toolshed I >> see two choices for a revision to select: >> >> 3:cdd9791c0afa >> 0:c1eeccec29d1 >> >> Which would I choose and why? >> >> Thanks, >> >> Greg >> >> On Fri, Feb 15, 2013 at 9:30 AM, James Taylor >> wrote: >> > The wrapper you are using is for MACS 1.3, there is a wrapper that is >> > compatible with 1.4 in the toolshed. >> > >> > -- >> > James Taylor, Assistant Professor, Biology/CS, Emory University >> > >> > >> > On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: >> >> Hi guys, >> >> >> >> I'm trying to run MACS in my local galaxy install (see screenshot: >> >> http://snag.gy/5QGUH.jpg) >> >> >> >> And I'm getting this error: >> >> >> >> Usage: macs <-t tfile> [-n name] [-g genomesize] [options] >> >> >> >> Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w >> >> --call-subpeaks >> >> >> >> macs: error: no such option: --lambdaset >> >> >> >> Thanks in advance for any help. >> >> >> >> -Greg >> >> >> >> Here's how I installed Macs (I guess it doesn't come built in?) >> >> >> >>> cd /usr/local/galaxy/downloads/ >> >>> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz >> >>> tar -xzvf MACS-1.4.2-1.tar.gz >> >>> cd MACS-1.4.2 >> >>> source /usr/local/galaxy/job_environment_setup_file >> >>> python setup.py install >> >>> deactivate >> >>> cd /misc/local/galaxy/galaxy_python/bin >> >>> ln -s macs14 macs >> >> >> >> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy >> >> user's path) >> >> ___ >> >> 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/ ___ 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/
Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
You likely want the newest version (3) On Feb 15, 2013 9:37 AM, "greg" wrote: > Thanks! So one question, when I go to install it from the toolshed I > see two choices for a revision to select: > > 3:cdd9791c0afa > 0:c1eeccec29d1 > > Which would I choose and why? > > Thanks, > > Greg > > On Fri, Feb 15, 2013 at 9:30 AM, James Taylor > wrote: > > The wrapper you are using is for MACS 1.3, there is a wrapper that is > > compatible with 1.4 in the toolshed. > > > > -- > > James Taylor, Assistant Professor, Biology/CS, Emory University > > > > > > On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: > >> Hi guys, > >> > >> I'm trying to run MACS in my local galaxy install (see screenshot: > >> http://snag.gy/5QGUH.jpg) > >> > >> And I'm getting this error: > >> > >> Usage: macs <-t tfile> [-n name] [-g genomesize] [options] > >> > >> Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w > --call-subpeaks > >> > >> macs: error: no such option: --lambdaset > >> > >> Thanks in advance for any help. > >> > >> -Greg > >> > >> Here's how I installed Macs (I guess it doesn't come built in?) > >> > >>> cd /usr/local/galaxy/downloads/ > >>> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz > >>> tar -xzvf MACS-1.4.2-1.tar.gz > >>> cd MACS-1.4.2 > >>> source /usr/local/galaxy/job_environment_setup_file > >>> python setup.py install > >>> deactivate > >>> cd /misc/local/galaxy/galaxy_python/bin > >>> ln -s macs14 macs > >> > >> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy > >> user's path) > >> ___ > >> 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/ > ___ 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/
Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
Thanks! So one question, when I go to install it from the toolshed I see two choices for a revision to select: 3:cdd9791c0afa 0:c1eeccec29d1 Which would I choose and why? Thanks, Greg On Fri, Feb 15, 2013 at 9:30 AM, James Taylor wrote: > The wrapper you are using is for MACS 1.3, there is a wrapper that is > compatible with 1.4 in the toolshed. > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: >> Hi guys, >> >> I'm trying to run MACS in my local galaxy install (see screenshot: >> http://snag.gy/5QGUH.jpg) >> >> And I'm getting this error: >> >> Usage: macs <-t tfile> [-n name] [-g genomesize] [options] >> >> Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w >> --call-subpeaks >> >> macs: error: no such option: --lambdaset >> >> Thanks in advance for any help. >> >> -Greg >> >> Here's how I installed Macs (I guess it doesn't come built in?) >> >>> cd /usr/local/galaxy/downloads/ >>> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz >>> tar -xzvf MACS-1.4.2-1.tar.gz >>> cd MACS-1.4.2 >>> source /usr/local/galaxy/job_environment_setup_file >>> python setup.py install >>> deactivate >>> cd /misc/local/galaxy/galaxy_python/bin >>> ln -s macs14 macs >> >> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy >> user's path) >> ___ >> 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/ ___ 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/
Re: [galaxy-dev] Problem using NGS: Peak Calling - MACS
The wrapper you are using is for MACS 1.3, there is a wrapper that is compatible with 1.4 in the toolshed. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Feb 15, 2013 at 9:26 AM, greg wrote: > Hi guys, > > I'm trying to run MACS in my local galaxy install (see screenshot: > http://snag.gy/5QGUH.jpg) > > And I'm getting this error: > > Usage: macs <-t tfile> [-n name] [-g genomesize] [options] > > Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w > --call-subpeaks > > macs: error: no such option: --lambdaset > > Thanks in advance for any help. > > -Greg > > Here's how I installed Macs (I guess it doesn't come built in?) > >> cd /usr/local/galaxy/downloads/ >> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz >> tar -xzvf MACS-1.4.2-1.tar.gz >> cd MACS-1.4.2 >> source /usr/local/galaxy/job_environment_setup_file >> python setup.py install >> deactivate >> cd /misc/local/galaxy/galaxy_python/bin >> ln -s macs14 macs > > (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy > user's path) > ___ > 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/ ___ 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/
[galaxy-dev] Problem using NGS: Peak Calling - MACS
Hi guys, I'm trying to run MACS in my local galaxy install (see screenshot: http://snag.gy/5QGUH.jpg) And I'm getting this error: Usage: macs <-t tfile> [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset Thanks in advance for any help. -Greg Here's how I installed Macs (I guess it doesn't come built in?) > cd /usr/local/galaxy/downloads/ > wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz > tar -xzvf MACS-1.4.2-1.tar.gz > cd MACS-1.4.2 > source /usr/local/galaxy/job_environment_setup_file > python setup.py install > deactivate > cd /misc/local/galaxy/galaxy_python/bin > ln -s macs14 macs (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy user's path) ___ 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/
Re: [galaxy-dev] Error while writing data in tophat2
Jeremy, But the tophat2 is running successfully in the command line. So, I guess it's related to Galaxy. Why am I getting this error in Galaxy? Is it because I don't have latest Galaxy? Is it file permission issue? I am using Tophat V2.0.7 and latest Bowtie2 version. On Fri, Feb 15, 2013 at 8:02 PM, Jeremy Goecks wrote: > This is not a known bug. For questions related to Tophat errors, you might > try the Tophat mailing list: > > tophat.cuffli...@gmail.com > > Good luck, > J. > > On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote: > > Galaxy is working fine in command line whereas in Galaxy at last i got > this error: > > > [2013-02-15 01:39:12] Reporting output tracks > [FAILED] > > Error running /usr/local/bin/tophat_reports --min-anchor 8 > --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50 > --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 > --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 > --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 > --min-coverage-intron 50 --max-coverage-intron 2 --min-segment-intron 50 > --max-segment-intron 50 --read-mismatches 2 --read-gap-length 2 > --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 > --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search > --no-microexon-search --sam-header > ./tophat_out/tmp/genome_genome.bwt.samheader.sam > --report-discordant-pair-alignments --report-mixed-alignments > --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 > --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 > --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 > /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa > ./tophat_out/junctions.bed ./tophat_out/insertions.bed > ./tophat_out/deletions.bed ./tophat_out/fusions.out > ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam > Loading ...done > > > Is it a known bug? > > ___ > 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/ > > > ___ 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/
Re: [galaxy-dev] Error while writing data in tophat2
This is not a known bug. For questions related to Tophat errors, you might try the Tophat mailing list: tophat.cuffli...@gmail.com Good luck, J. On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote: > Galaxy is working fine in command line whereas in Galaxy at last i got this > error: > > > [2013-02-15 01:39:12] Reporting output tracks > [FAILED] > Error running /usr/local/bin/tophat_reports --min-anchor 8 > --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50 > --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 > --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 > --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 > --min-coverage-intron 50 --max-coverage-intron 2 --min-segment-intron 50 > --max-segment-intron 50 --read-mismatches 2 --read-gap-length 2 > --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 > --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search > --no-microexon-search --sam-header > ./tophat_out/tmp/genome_genome.bwt.samheader.sam > --report-discordant-pair-alignments --report-mixed-alignments > --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 > --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 > --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 > /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa > ./tophat_out/junctions.bed ./tophat_out/insertions.bed > ./tophat_out/deletions.bed ./tophat_out/fusions.out > ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam > Loading ...done > > Is it a known bug? > ___ > 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/ ___ 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/
Re: [galaxy-dev] hg19 reference gnome for Tophat2
Now try running the test data in Galaxy to see if you get the same results. You should probably try running from the history first and then try adding the test data as a built-in genome via the bowtie2_indexes.loc table Best, J. On Feb 15, 2013, at 12:18 AM, Sachit Adhikari wrote: > Hi Jeremy, > > I was successfully able to run the test data from the tophat2 website in > command line. I think there's something wrong with the reference genome. I > have correctly specified the path of reference genome? What's the problem I > am facing? > > On Thu, Feb 14, 2013 at 1:44 PM, Jeremy Goecks > wrote: > Try using the Tophat test data to verify your installation; it's known to > have splice junctions: > > http://tophat.cbcb.umd.edu/tutorial.html > http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz > > Good luck, > J. > > On Feb 14, 2013, at 6:29 AM, Sachit Adhikari wrote: > >> I tried with many data but still the same problem and regarding settings I >> haven't changed a thing of Tophat2. What might be causing this error? >> >> Thanks >> >> On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks >> wrote: >> If the other outputs are fine, then the problem is likely with your data >> and/or your Tophat settings. >> >> Good luck, >> J. >> >> On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote: >> >>> Ok sorry. I did that, but the output of splice junctions is empty. The >>> other outputs looks fine. What might be the problem? >>> >>> Thanks, >>> >>> Sachit >>> >>> On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks >>> wrote: >>> > Shall I replace: >>> > >>> > /orig/path/hg19hg19hg19 >>> > /depot/data2/galaxy/bowtie2/hg19/hg19 >>> > >>> > with >>> > >>> > hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index >>> >>> Yes, that's correct. >>> >>> Finally, please email only galaxy-dev with questions about local >>> installations; galaxy-user is for questions about how to use Galaxy. >>> >>> Best, >>> J. >>> >>> >> >> > > ___ 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/
Re: [galaxy-dev] can't run instance for CloudMan
Stefano, Sounds like it's most likely that the security groups aren't configured correctly. What I'd recommend would be to launch your instance using http://usegalaxy.org/cloudlaunch which does all of those configuration steps for you automatically. -Dannon On Feb 14, 2013, at 8:28 PM, stefano cardinale wrote: > Hi, I am having a problem with running galaxy on the Amazon cloud. I have > tried this several times over the past few days, I followed the list and it > seems my instance is up and running. However, when I type the DNS in any > browser it can't connect to it. I am kind of aiming in the dark now because I > don't know where the problem is, anyone can help? > thanks! > stefano > > > > > > > > ___ > 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/ ___ 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/
Re: [galaxy-dev] environment variables and paths for toolshed tools
>> On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
>>
>> Are there any environment variables that are honored by toolshed installed
>> tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
>> $GALAXY_HOME, then uploaded it the test toolshed, then installed it
>> automatically. Neither of these resolved to what I expected. I don't want
>> to hard-code the path in the xml tool file, but rather have a default
>> location for other executables and jar files. How should this best be done?
>>
>> David Hoover
>> Helix Systems Staff
On Wed, Sep 12, 2012 at 6:15 PM, Greg Von Kuster wrote:
> Hello David,
>
> This is not currently possible, but will be available in the next Galaxy
> distribution release, currently scheduled for about 10 days from now. You
> will include a tool_dependencies.xml file in your tool shed repository that
> looks something like the following.
>
>
>
>
> action="set_to">$INSTALL_DIR
>
>
>
> Your tool will find the required files via the defined JAVA_JAR_PATH by
> using a tag set in the tool config, something like this:
>
>
> JAVA_JAR_PATH
>
>
> The tag in the tool config would be something like this:
>
>
> python_wrapper.py $JAVA_JAR_PATH/some_file.jar $param1 $param2...
>
>
> I'm close to having this working, so if you are interested in testing before
> the next Galaxy dist release, let me know and I'll tell you when the Galaxy
> central repository has the new feature.
>
> Thanks!
>
> Greg Von Kuster
Hi guys,
Reading the rest of the thread from December, Greg's new code did
get checked in and should be working (I've not tried this yet).
However, I can't help feeling that defining the two environment variables
David suggested, $GALAXY_DATA_INDEX_DIR and/or $GALAXY_HOME,
would cover the majority of use cases and be far simpler for tool authors
to use. Am I overlooking something?
Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
say motif.dat) which is used by a script (say motif.py) via a normal
Galaxy tool XML file (say motif.xml).
Perhaps I can just put my data file next to the script and XML file, in
which case it is easy for the script to locate? But I assumed that
Galaxy best practice would be to use the tool-data folder somehow...
Thanks,
Peter
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[galaxy-dev] Fwd: Error while writing data in tophat2
-- Forwarded message -- From: Sachit Adhikari Date: Fri, Feb 15, 2013 at 11:02 AM Subject: Error while writing data in tophat2 To: galaxy-dev@lists.bx.psu.edu Galaxy is working fine in command line whereas in Galaxy at last i got this error: [2013-02-15 01:39:12] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 2 --min-segment-intron 50 --max-segment-intron 50 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done Is it a known bug? ___ 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/
Re: [galaxy-dev] can't run instance for CloudMan
Hi Stefano, Can you try out what we put together: https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Thu, Feb 14, 2013 at 8:28 PM, stefano cardinale wrote: > Hi, I am having a problem with running galaxy on the Amazon cloud. I have > tried this several times over the past few days, I followed the list and it > seems my instance is up and running. However, when I type the DNS in any > browser it can't connect to it. I am kind of aiming in the dark now because I > don't know where the problem is, anyone can help? > thanks! > stefano > > > > > > > > ___ > 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/ ___ 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/
[galaxy-dev] Error while writing data in tophat2
Galaxy is working fine in command line whereas in Galaxy at last i got this error: [2013-02-15 01:39:12] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 50 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 2 --min-segment-intron 50 --max-segment-intron 50 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done Is it a known bug? ___ 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/
