[galaxy-dev] Composite Datatype (auto_primary_file) not uploading
Dear all,
We have a modified Galaxy server with tools for virtual screening. You can
access is at http://lisis.cs.ucy.ac.cy.
We created a composite datatype (auto_primary_file) to handle PDBQT files
for proteins and their config file requested by AutoDock Vina, in simple
words is a composite datatype consisted of two files, a pdbqt file and a
text file.
We have the following problems:
1. Uploading the files needed to create such a composite datatype via
the Upload Tool, stacks in upload phase, as shown in the following figure
http://prntscr.com/xbosn
1. As you can see in the figure, uploading individual files works
2. In this figure http://prntscr.com/xbp6k you can see the upload
options for this composite datatype.
2. Uploading composite datatypes within a data library does not provide
the same functionality as the Upload Tool.
Regarding problem 1 what do you think is the underlying problem?
Following is the source code of this composite datatype class:
class PDBQT_Protein(Html):
PDBQT Protein files, ASCII protein information files.
MetadataElement(name = base_name, desc = Base name for all
transformed versions of this PDBQT protein dataset, default = 'protein',
readonly = False, set_in_upload = True)
composite_type = 'auto_primary_file'
allow_datatype_change = False
file_ext = 'pdbqt_protein'
def __init__(self, **kwd):
Text.__init__(self, **kwd)
self.add_composite_file('%s.pdbqt', description = 'PDBQT Protein
File', substitute_name_with_metadata = 'base_name', mimetype =
'text/plain', is_binary = False)
self.add_composite_file('%s_config.txt', description = 'PDBQT
Config File', substitute_name_with_metadata = 'base_name', mimetype =
'text/plain', is_binary = False)
def generate_primary_file(self, dataset = None):
if dataset.metadata.base_name == protein and \
dataset.metadata.base_name != dataset.name:
dataset.metadata.base_name = dataset.name
rval = ['htmlheadtitlePDBQT Protein Galaxy/LiSIs Composite
Dataset/title/head']
rval.append('bodydivThis %s composite dataset is composed of
the following files:ul' % (dataset.metadata.base_name))
for composite_name, composite_file in
self.get_composite_files(dataset = dataset).iteritems():
fn = composite_name
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
if composite_file.get('description'):
rval.append('lia href=%s%s (%s)/a%s/li' % (fn,
fn, composite_file.get('description'), opt_text))
else:
rval.append('lia href=%s%s/a%s/li' % (fn, fn,
opt_text))
rval.append('/ul/div/body/html')
return \n.join(rval)
def regenerate_primary_file(self, dataset):
cannot do this until we are setting metadata
bn = dataset.metadata.base_name
efp = dataset.extra_files_path
flist = os.listdir(efp)
rval = ['htmlheadtitlePDBQT Protein Galaxy/LiSIs Composite
Dataset/title/head']
rval.append('bodydivThis %s composite dataset is composed of
the following files:ul' % (bn))
for i, fname in enumerate(flist):
sfname = os.path.split(fname)[-1]
rval.append('lia href=%s%s/a/li' % (sfname, sfname))
rval.append('/ul/div/body/html')
f = file(dataset.file_name, 'w')
f.write(\n.join(rval))
f.write('\n')
f.close()
def set_meta(self, dataset, **kwd):
Set metadata...
Text.set_meta(self, dataset, **kwd)
if dataset.metadata.base_name == protein and \
dataset.metadata.base_name != dataset.name:
dataset.metadata.base_name = dataset.name
log.debug('@@@ PDBQT_Protein set_meta changed
dataset.metadata.base_name to: %s' % (dataset.metadata.base_name))
if kwd.get('overwrite') == False:
log.debug('@@@ PDBQT_Protein set_meta called with overwrite =
False')
return True
try:
efp = dataset.extra_files_path
except:
log.debug('@@@ PDBQT_Protein set_meta failed %s - dataset %s
has no extra_files_path ?' % (sys.exc_info()[0], dataset.name))
return False
try:
flist = os.listdir(efp)
except:
log.debug('@@@ PDBQT_Protein set_meta failed %s - dataset %s
has no extra_files_path ?' % (sys.exc_info()[0], dataset.name))
return False
if len(flist) == 0:
log.debug('@@@ PDBQT_Protein set_meta failed - %s
extra_files_path %s is empty?' % (dataset.name, efp))
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy/LiSIs %s PDBQT Protein datatype object'
% (dataset.metadata.base_name)
if not dataset.blurb:
dataset.blurb = 'Composite file - %s PDBQT Protein Galaxy/LiSIs
[galaxy-dev] Setting up Cloudman instance
Hi Team, I am working on setting up a Cloudman instance for a course we are preparing. I have used the link provided: http://usegalaxy.org/cloudlaunch and can get an instance running. The issues are as follow: 1. I need to add tools and have not found a clear method in doing so utilizing the galaxy toolshed. 2. Once I have the instance setup and shut it down I cannot restart it cleanly. On restart it appears that nginx fails to launch since port 80 is not listening. I have not found a way to start it manually. 3. I have followed both the above provided url to setup an instance and the instructions at http://wiki.galaxyproject.org/CloudMan and have had the same results. I have read a few posts of similar issues, but have not found a solution. Any suggestions will be helpful. Thanks, Iry Witham __ Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.wit...@jax.org The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Setting up Cloudman instance
On Fri, Mar 22, 2013 at 8:40 AM, Iry Witham iry.wit...@jax.org wrote: I am working on setting up a Cloudman instance for a course we are preparing. I have used the link provided: http://usegalaxy.org/cloudlaunch and can get an instance running. The issues are as follow: 1. I need to add tools and have not found a clear method in doing so utilizing the galaxy toolshed. Until the new release of Cloudman there are a few manual steps you need to take if you want to get an instance started that's compatible with the toolshed interface. Starting with a fresh Galaxy type instance, launched via usegalaxy.org/cloudlaunch: Update Galaxy. You can do this through the admin panel (your_instance/cloud/admin), or by ssh'ing in and pulling. The cloud instances previously tracked galaxy-central, though you'll probably want to pull from -dist now. Depending on how far you update (current -central tip for sure) this may not merge all changes to run.sh cleanly. You'll need to ssh in and add the additional .sample files. You should be able to simply `hg diff run.sh` and then edit the file to add the missing samples. While ssh'ed in, edit universe_wsgi.ini to both add yourself as an admin user and configure the tool_config_file entry to look like this: tool_config_file = tool_conf.xml,shed_tool_conf.xml Now back in the cloudman admin interface, you'll want to find the galaxy service and 'update db', and then 'restart' galaxy, potentially having to 'restart' two times if tool migrations were included in your update (these throw an exception at launch and exit, printing stuff to the log). After that, unless I've forgotten something, you should be good to go. 2. Once I have the instance setup and shut it down I cannot restart it cleanly. On restart it appears that nginx fails to launch since port 80 is not listening. I have not found a way to start it manually. Stopping and starting an instance via the AWS console isn't supported, it'll definitely break things. Instead, just use the terminate cluster functionality in the primary cloudman interface. By default all of the galaxy data (/mnt/galaxyData) is persisted. If you have made modifications to the galaxyTools volume (by either manually installing tools or using the toolshed to do so) you'll need to click persist galaxyTools in the cloudman admin interface -- this is just once, after modifications are done or tools are installed as you want them. Of course, if you never want to use a cluster again and want to clean up all saved data (both S3 and EBS) just check Delete Permanently in cluster shutdown. Good luck, and let me know if I've left anything out of my instructions above and I'll do what I can to help! Dannon ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] user-specific tool panel
Hi guys, I'm wondering whether it is possible to have user-specific tool panels after logging in. This way users could customize the tool panel for instance by increasing the visibility of their (user-specific) favorites ... This would be a wonderful feature. However searching in the documentation and the mailing list, I did not find anything. Hence, it would be great if anybody could give me a hint or if impossible to mark this as a feature request. Thanks for any help. Jens ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Displaying track into UCSC (update)
Hi Dan, I just updated our sources and… it works ! Thanks a lot, Regards, Julien Le 21 mars 2013 à 16:30, Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu a écrit : Hi Julien, This was fixed in changeset 6cd4058d7b32 (https://bitbucket.org/galaxy/galaxy-dist/commits/6cd4058d7b32/). Can you update your Galaxy instance and see if the issue is resolved for you? Thanks for using Galaxy, Dan On Mar 20, 2013, at 4:53 AM, Julien SEILER wrote: Hello Carl, We are using galaxy-dist on revision a4113cc1cb5e. When we talk about private dataset, we mean datasets that have been uploaded to a user history through the Upload file tool. The access permission is allowed only to the current user role for these datasets. Anonymous user are not allowed on our galaxy instance. Regards, Julien Le 19 mars 2013 à 22:45, Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com a écrit : Hello, Stephanie and Julien What revision are you using IGBMC? Can you clarify what you mean by a private dataset? Are non-owners importing into a history via a shared history, or are they being passed a direct link to the UCSC display viewer from the owner? Thanks for the information, Carl On Tue, Mar 19, 2013 at 1:27 PM, Stephanie LE GRAS sleg...@igbmc.frmailto:sleg...@igbmc.fr wrote: Hi all, Here is an update regarding the problem we are facing with Julien with our local instance of Galaxy. As Julien said we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) We have worked for hours on it today and we have identified that datasets that can be uploaded to UCSC are actually public datasets and that Julien can upload all his datasets to UCSC because they are all public by default. What is interesting now is that we've seen that the path to the data in the UCSC error message is : http://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interv al_as_bed/main/bea5029fce8b957e/data/galaxy.bedhttp://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interval_as_bed/main/bea5029fce8b957e/data/galaxy.bed: While it should be : http://www.galaxy-igbmc.fr/display_at(Š)/galaxy.bedhttp://www.galaxy-igbmc.fr/display_at(%C5%A0)/galaxy.bed Because the right function to use in order to check whether the dataset can be uploaded to UCSC should be display_at but not display_application. Any ideas of what could cause Galaxy not to use the right function? Thank you in advance, Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73tel:%2B33%20%280%293%2088%2065%2032%2073 Tel. Solexa : +33 (0)3 88 65 32 97tel:%2B33%20%280%293%2088%2065%2032%2097 Le 18/03/13 19:20, « Julien SEILER » seil...@igbmc.frmailto:seil...@igbmc.fr a écrit : Hi all, We have installed a local galaxy server and we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) Curiously, it works fine with my personal account but it doesn't for all other users. It also works for displaying tracks based on a public dataset for all users. Could anybody explain us what's happening ? Thanks in advance for any help, Julien ___ 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/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)
I have been running a Galaxy server for our sequencing researchers for a while now and it's become increasingly successful. The biggest resource challenge for us has been, and continues to be disk space. As such, I'd like to implement some additional cleanup scripts. I thought I run a few questions by this list before I got too far into things. In general, I'm wondering how to implement updates/additions to the cleanup system that will be in line with the direction that the Galaxy project is headed. The pgcleanup.py script is the newest piece of code in this area (and even adds cleanup of exported histories, which are absent from the older cleanup scripts). Also, the pgcleanup.py script uses a cleanup_event table that I don't believe is used by the older cleanup_datasets.py script. However, the new pgcleanup.py script only works for Postgres, and worse, only for version 9.1+. I run my system on RedHat (CentOS) and thus we use version 8.4 of Postgres. Are there plans to support other databases or older versions of Postgres? I'd like to implement a script to delete (set the deleted flag) for certain datasets (e.g. raw data imported from our archive, for old, inactive users, etc.). I'm wondering if it would make sense to try and extend pgcleanup.py or cleanup_datasets.py. Or perhaps it would be best to just implement a separate script, though that seems like I'd have to re-implement a lot of boilerplate code for configuration reading, connections, logging, etc. Any tips on generally acceptable (supported) procedures for marking a dataset as deleted? Of course, I'll make any of the enhancements available (and would be happy to submit pull requests if there is interest). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)
On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: I have been running a Galaxy server for our sequencing researchers for a while now and it's become increasingly successful. The biggest resource challenge for us has been, and continues to be disk space. As such, I'd like to implement some additional cleanup scripts. I thought I run a few questions by this list before I got too far into things. In general, I'm wondering how to implement updates/additions to the cleanup system that will be in line with the direction that the Galaxy project is headed. The pgcleanup.py script is the newest piece of code in this area (and even adds cleanup of exported histories, which are absent from the older cleanup scripts). Also, the pgcleanup.py script uses a cleanup_event table that I don't believe is used by the older cleanup_datasets.py script. However, the new pgcleanup.py script only works for Postgres, and worse, only for version 9.1+. I run my system on RedHat (CentOS) and thus we use version 8.4 of Postgres. Are there plans to support other databases or older versions of Postgres? Hi Lance, pgcleanup.py makes extensive use of Writable CTEs, so there is not really a way to port it to older versions. For 8.4 or MySQL, you can still use the older cleanup_datasets.py. I'd like to implement a script to delete (set the deleted flag) for certain datasets (e.g. raw data imported from our archive, for old, inactive users, etc.). I'm wondering if it would make sense to try and extend pgcleanup.py or cleanup_datasets.py. Or perhaps it would be best to just implement a separate script, though that seems like I'd have to re-implement a lot of boilerplate code for configuration reading, connections, logging, etc. Any tips on generally acceptable (supported) procedures for marking a dataset as deleted? You could probably reuse a lot of the code from either of the cleanup scripts for this. Thanks, --nate Of course, I'll make any of the enhancements available (and would be happy to submit pull requests if there is interest). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] redirection vulnerability via URL injection
Hi Vipin, Thank you for reporting this issue. This has to do with the way that the old-style (hard-coded) display applications were modified after introduction of roles to authorize access to an user's datasets that might be permission protected. Ideally, with these old-style applications, much of the work that is being done upfront on history load would be backended to happen after the user clicks to view a dataset -- e.g. the viewport is being generated for all datasets in a history, example link: http://localhost:8080/datasets/190/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dhg18%26position%3Dchr21%3A0-536870912%26hgt.customText%3D%25sdisplay_url=http%3A%2F%2Flocalhost%3A8080%2Froot%2Fdisplay_as%3Fid%3D190%26display_app%3Ducsc%26authz_method%3Ddisplay_at If redesigned so that everything happens after the user clicks the link, I see no reason why the redirect_url functionality could not be removed. As it stands now, the redirect url is %s substituted with the URL-encoded value that will contain the authorized URL to access the dataset (e.g. http://localhost:8080/root/display_as?id=190display_app=ucscauthz_method=display_at), and then the user is redirected there. I've added a Trello card (https://trello.com/c/uIctksud) for this issue. In the mean time, however, I have committed a patch to the stable branch that will allow administrators to disable the use of the old-style display applications. Thanks for using Galaxy, Dan On Mar 12, 2013, at 12:08 PM, Vipin TS wrote: Hello dev-members, We are trying to place our public Galaxy instance in a more secured manner, Currently I am playing with few test cases about the redirection vulnerabilities. The following link uses a URL variable called “redirect_url” to redirect a user to a given page. While this variable is intended to only direct a user to a trusted page, it fails to validate the provided value and therefore can be used to redirect to any page. http://localhost:8080/datasets/332056/display_at/ucsc_test?redirect_url=http://www.google.comdisplay_url=http://localhost:8080/root This example redirects a user to Google, but it could just as easily be used to direct a user to a page that contains any malware. To resolve the issue, may be validate all user controlled input, including the GET request variables. If the input is intended to redirect a user, it must be validated to ensure it only presents them with a page on the trusted site. any comments or suggestions to work around this. thanks --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy: Dependency error htseq_count
Glad that everything works now for you. The Get Updates functionality won't work since this is a new version of the tool (updated version of HTSeq package). Since the updated version could generate different results with the same input, Galaxy keeps the old version around for reproducibility reasons. I don't know why you have to restart Galaxy for the tool to show up. As far as I know, that should not be necessary, and also shouldn't be dependent on anything in the tool wrapper configuration. I'm aware of the issue with the screenshot missing. I'm not sure how to get the tool wrapper to point to the static images installed from the toolshed (or if that's even possible). In the meantime, a workaround would be to copy the count_modes.png file from the repository to the [GALAXY_HOME]/static/images directory. Lance Joachim Jacob | VIB | wrote: *sorry for my late reply - we have experienced some email issues lately * Thanks, a clean install from the new versions works! Unfortunately, the 'get updates' from the admin interface of Galaxy does not find any updates with the old version. So, I searched the main toolshed, and I was able to install the new version next to the old (instead of updating). The install succeeded, but I always have to restart Galaxy to get the tool available in the toolbox. One small remark: the screenshot in the tool's interface below the parameters is not shown. Cheers Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/11/2013 06:34 PM, Lance Parsons wrote: I have posted an updated version of the htseq-count tool in the toolshed that uses and updated version of the HTSEQ count package (0.5.4p1) and hopefully addresses the installation issue you have experienced. Please try it out and let me know if you still have problems. Lance Joachim Jacob | VIB | wrote: Hi Lance, [apologies for directly emailing to you and not through the galaxy-dev list. I will post it on the dev list later on] I am trying to install htseq-count, but it fails during the dependency installation of htseq. The error I get is: error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). Any idea whether it is related to my setup (and what I can do about it)? Note: only the htseq_count dependency is not being installed. Thanks for providing the htseq_count wrapper! Now getting it through the toolshed will make it again a little closer to a perfect world :-) Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking into this Greg. The environment where I'm having this problem is our testing and production systems. Both environments are CentOS release 5.8 (Final) with Mercurial version 2.4.1. Interestingly, when I tried the same thing with a development setup on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same issue. One difference is that on my testing/production boxes I do have an older version of the tool installed, so perhaps that is the issue. I also tried uninstalling, but that led to the (expected) error that that a previous changeset is installed: The tool shed repository htseq_count with owner lparsons and changeset revision f320093f1e8e was previously installed using changeset revision 5d969cb56112. The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. You can get the latest updates for the repository using the Get updates option from the repository's Repository Actions pop-up menu. Click here to manage the repository. I then attempted to reinstall and I got a javascript message the cloning failed, and the repo is now stuck in the cloning state. I did not see anything in the paster logs regarding this at all. Here are the steps I took on my local system: 1. Upload htseq-count v0.3 to local toolshed 2. Install on local galaxy 3. Upload htseq-count v0.3-release2 to toolshed [Errno 2] No such file or directory: '/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' STDOUT from paster
[galaxy-dev] Toolshed - Installation of static files
For one of my tool wrappers (htseq-count) in the toolshed, I point to an image file in the Help section. At the moment, I'm including the image in the repository as static/imagescount_modes.png and pointing to it in the wrapper.xml file with .. image:: /static/images/count_modes.png. However, the toolshed installation doesn't copy this file to the static directory of the galaxy install (which doesn't seem like a good idea anyway). Is there any way for me to include a static file and then point to that file in the help when the tool is installed automatically via the toolshed.. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed - Installation of static files
Hi Lance, I answered this in your previous email - here's the answer: To make this work in the tool shed, make the static directory that contains the image file a relative path in the tool config. For example, your repository has the following structure: htseq_count htseq-count.xml sam_fa_indices.loc.sample static/ images/ count_modes.png test-data/ tool_data_table_conf.xml.sample tool_dependencies.xml The help section of your tool config should simply use a relative path to the image file ( in this case, just a a . in front of the path to the image file ) .. image:: ./static/images/count_modes.png :width: 500 I believe that's all that is necessary. Greg Von Kuster On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote: For one of my tool wrappers (htseq-count) in the toolshed, I point to an image file in the Help section. At the moment, I'm including the image in the repository as static/imagescount_modes.png and pointing to it in the wrapper.xml file with .. image:: /static/images/count_modes.png. However, the toolshed installation doesn't copy this file to the static directory of the galaxy install (which doesn't seem like a good idea anyway). Is there any way for me to include a static file and then point to that file in the help when the tool is installed automatically via the toolshed.. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed - Installation of static files
Thanks for the quick response Greg. I tried this and uploaded an update to the testtoolshed and installed that in a test instance of Galaxy. Unfortunately, it didn't seem to resolve the issue. Galaxy still renders the html with the image source pointing to the same location (e.g. http://127.0.0.1:8080/static/images/count_modes.png). This doesn't resolve. You can try installing the htseq_count package from the testtoolshed to see the issue for yourself. Lance Greg Von Kuster wrote: Hi Lance, I answered this in your previous email - here's the answer: To make this work in the tool shed, make the static directory that contains the image file a relative path in the tool config. For example, your repository has the following structure: htseq_count http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# htseq-count.xml http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# sam_fa_indices.loc.sample http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# static/ http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# images/ http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# count_modes.png http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# test-data/ http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# tool_data_table_conf.xml.sample http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# tool_dependencies.xml http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224# The help section of your tool config should simply use a relative path to the image file ( in this case, just a a . in front of the path to the image file ) .. image:: ./static/images/count_modes.png :width: 500 I believe that's all that is necessary. Greg Von Kuster On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote: For one of my tool wrappers (htseq-count) in the toolshed, I point to an image file in the Help section. At the moment, I'm including the image in the repository as static/imagescount_modes.png and pointing to it in the wrapper.xml file with .. image:: /static/images/count_modes.png. However, the toolshed installation doesn't copy this file to the static directory of the galaxy install (which doesn't seem like a good idea anyway). Is there any way for me to include a static file and then point to that file in the help when the tool is installed automatically via the toolshed.. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed - Installation of static files
Hello Lance, Sorry this didn't work. I've opened the following Trello card for this issue. https://trello.com/card/toolshed-handle-images-defined-in-help-sections-of-tool-configs-contained-in-a-repository/506338ce32ae458f6d15e4b3/725 Thanks, Greg Von Kuster On Mar 22, 2013, at 1:50 PM, Lance Parsons wrote: Thanks for the quick response Greg. I tried this and uploaded an update to the testtoolshed and installed that in a test instance of Galaxy. Unfortunately, it didn't seem to resolve the issue. Galaxy still renders the html with the image source pointing to the same location (e.g. http://127.0.0.1:8080/static/images/count_modes.png). This doesn't resolve. You can try installing the htseq_count package from the testtoolshed to see the issue for yourself. Lance Greg Von Kuster wrote: Hi Lance, I answered this in your previous email - here's the answer: To make this work in the tool shed, make the static directory that contains the image file a relative path in the tool config. For example, your repository has the following structure: htseq_count htseq-count.xml sam_fa_indices.loc.sample static/ images/ count_modes.png test-data/ tool_data_table_conf.xml.sample tool_dependencies.xml The help section of your tool config should simply use a relative path to the image file ( in this case, just a a . in front of the path to the image file ) .. image:: ./static/images/count_modes.png :width: 500 I believe that's all that is necessary. Greg Von Kuster On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote: For one of my tool wrappers (htseq-count) in the toolshed, I point to an image file in the Help section. At the moment, I'm including the image in the repository as static/imagescount_modes.png and pointing to it in the wrapper.xml file with .. image:: /static/images/count_modes.png. However, the toolshed installation doesn't copy this file to the static directory of the galaxy install (which doesn't seem like a good idea anyway). Is there any way for me to include a static file and then point to that file in the help when the tool is installed automatically via the toolshed.. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Uploading large data sets from cluster file system for local galaxy install
Hello, I have a question for the many galaxy admins here. I am in the process of setting up a local galaxy install submitting the jobs as real users to our local SGE cluster. I am trying to figure out the best way to load large datasets (Sequence files etc..) stored in the local clusters storage. These files might not be world readable and we cannot assume that the user knows how to make it so. I was wondering if anybody here has tackled the problem and found a workable solution? Thanks, -Raj ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)
Nate Coraor wrote: On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: I have been running a Galaxy server for our sequencing researchers for a while now and it's become increasingly successful. The biggest resource challenge for us has been, and continues to be disk space. As such, I'd like to implement some additional cleanup scripts. I thought I run a few questions by this list before I got too far into things. In general, I'm wondering how to implement updates/additions to the cleanup system that will be in line with the direction that the Galaxy project is headed. The pgcleanup.py script is the newest piece of code in this area (and even adds cleanup of exported histories, which are absent from the older cleanup scripts). Also, the pgcleanup.py script uses a cleanup_event table that I don't believe is used by the older cleanup_datasets.py script. However, the new pgcleanup.py script only works for Postgres, and worse, only for version 9.1+. I run my system on RedHat (CentOS) and thus we use version 8.4 of Postgres. Are there plans to support other databases or older versions of Postgres? Hi Lance, pgcleanup.py makes extensive use of Writable CTEs, so there is not really a way to port it to older versions. For 8.4 or MySQL, you can still use the older cleanup_datasets.py. After looking at it a bit more, I see what you mean. Are there plans to implement and additional cleanup scripts for non-postgres 9.1 users? Just curious so I don't reinvent the wheel, I'd be happy to help with existing efforts. I'd like to implement a script to delete (set the deleted flag) for certain datasets (e.g. raw data imported from our archive, for old, inactive users, etc.). I'm wondering if it would make sense to try and extend pgcleanup.py or cleanup_datasets.py. Or perhaps it would be best to just implement a separate script, though that seems like I'd have to re-implement a lot of boilerplate code for configuration reading, connections, logging, etc. Any tips on generally acceptable (supported) procedures for marking a dataset as deleted? You could probably reuse a lot of the code from either of the cleanup scripts for this. Right. It seems to make sense to me to focus on the cleanup_datasets.py since that will work for everyone. I would like to essentially mimic the user deleting a dataset. I'd then email them to let them know that some old data had been marked for deletion and let the rest of the scripts proceed as normal, cleaning that up if they don't undelete it. It looks like I would want to mark the HistoryDatasetAssociations as deleted? Is that correct? Would I need to do anything else to simulate the user deleting the dataset? Thanks for the help, Lance Thanks, --nate -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] History periodically disappears in AWS Cloudman installation
Hi, We're running a private Cloudman Galaxy on AWS for small-scale proteomics work. Lately the whole History of the main user id we use has occasionally disappeared, ie. on login the History is empty. The datasets aren't hiding in Deleted Datasets. They appear to still be there in /mnt/galaxyData/files/000. They're not in the Anonymous (not logged in ) id. They're not in another id. The data doesn't come back later. We reload the latest datasets in use and the numbering in the history restarts from 1. We're running the most basic config, with the simple single-threaded database. Nothing of interest seems to be in the various Cloudman logs. I've searched the archives for lost/deleted/disappeared datasets/history etc but nothing useful turned up. This is our rev status .. UBUNTU /mnt/galaxyTools/galaxy-central $ hg summary parent: 8116:ecd131b136d0 tip libraries: fix in query for 'datasets_are_public' branch: default commit: 2 modified, 268 unknown update: (current) This is a poor fault report but .. appreciate any pointers here. Many thanks ... -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] user-specific tool panel
Jens, This isn't possible right now but has been suggested in the past. I've created a Trello card for the idea that you can comment/vote on: https://trello.com/c/zQcLM6I4 Best, J. On Mar 22, 2013, at 6:04 AM, Keilwagen, Jens wrote: Hi guys, I'm wondering whether it is possible to have user-specific tool panels after logging in. This way users could customize the tool panel for instance by increasing the visibility of their (user-specific) favorites ... This would be a wonderful feature. However searching in the documentation and the mailing list, I did not find anything. Hence, it would be great if anybody could give me a hint or if impossible to mark this as a feature request. Thanks for any help. Jens ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
