Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content
Hi, On Jul 27, 2011, at 3:34 PM, Peter Cock wrote: On Wed, Jul 27, 2011 at 2:28 PM, Greg Von Kuster g...@bx.psu.edu wrote: Helo Jelle, I've taken a look at your patches and the code looks good. However, I'm wondering why you find it necessary to upload image files to Galaxy. Do tools exist that take image files as input? If the Galaxy community finds this feature as a good addition to Galaxy, we can probably incorporate it into the distribution. I think it is a nice feature - and can come up with some use cases too. +1 How about future tools for image analysis? e.g. microscope photos of cultures to automatically do cell/organism counting, or plant leaves for pathogenicity assays. However, we'll need an additional feature before we can do that. We'll need to implement a type of config setting that enables / disables the uploading of image files via the Galaxy api. ... Why not just allow it? Indeed! A general configuration allowing/blocking any file type from being uploaded makes more sense to me than just wanting to block images. Why block file types? If you really want to then how about automagically *allowing* all file types specified in datatypes_conf.xml? Cheers, Pi 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Wrapper generator.
Hi Jeroen, You can use web services thanks to the work from Sumedha Ganjoo et al. from the University of Georgia. You can find that on the community site: Tools Shed - Data Source - Suite of Web service addition tools. http://community.g2.bx.psu.edu/common/view_tool?sort=suitecntrller=toolwebapp=communityoperation=view_toolid=1766c85c07803d78 Cheers, Pi On May 13, 2011, at 1:41 PM, J. F. J. Laros wrote: Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] User Name not set with external LDAP authentication
Hi Leandro, On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote: Hi Pieter, cut I have this *exact* same setup as you where I am authenticating with the LDAP user ID and returning a mail LDAP attribute as REMOTE_USER, but this sets the Galaxy user email address (which in Galaxy is the user ID) but is *doesn't* set any *User Name*, all my external users have User Name not set. Are you sure your setup above sets the User Name to something? Check under Admin - Manage Users, under the User Name column all my users that are external yes say not set. Sorry for the confusion. Indeed it's the user ID alias e-mail address that is set correctly. The user name is not set and I don't know how to set it or if that is even possible with the current Galaxy Maybe some of the developers can enlighten us... Cheers, Pi regards, Leandro - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
Hi Jeff, 1. As Florent wrote, probably the easiest solution is to install the dependencies with MacPorts. Only if stuff is not available via MacPorts or the version available is too old / incompatible with other dependencies I install things manually. MacPorts will add a line like this: - export PATH=/opt/local/bin:/opt/local/sbin:$PATH - to your ~/.profile file, which is automatically sourced when you open a new Terminal window. Galaxy is probably running using a different account than yours. Usually a dedicated one or one used for the webserver like _www or www or apache or ... This user must have the same addition to it's environment in order to find gnuplot et al. To give Galaxy the same environment you can either add the line above to galaxy/run.sh immediately after the first line that identifies the file as a shell script (#!/bin/sh) and before the code that starts Galaxy. Optionally you may specify the environment in a separate file and source this file. Personally I like the latter, because I can manage the environment for multiple users and software packages in a single file that I can call from various locations. To source a file you use the . command. Hence [dot][space][path to env file]. Your galaxy/run.sh would start like this: - #!/bin/sh # # Source my custom environment including the path to MacPorts and other stuff I installed outside the default search paths # . /path/to/our_environment.bashrc - In our_environment.bashrc you would than have the same line: export PATH=/opt/local/bin:/opt/local/sbin:$PATH and potentially other stuff to set your environment. 2. For the gnuplot error below unknown or ambiguous terminal type: It seems the gnuplot script Galaxy is calling is trying to use an unsupported terminal. When you save the figure to a file a terminal is just a file type. In order to write jpeg, tiff, png, pdf, svg, etc. images gnuplot uses several libraries. When you install gnuplot it will look which libraries are available and based on that some image file formats may be available and others will not. It seems png support is not available. When you start a gnuplot terminal and type 'set terminal' for a list, do you see png as a supported terminal? If not, you should probably install libpng first and re-compile gnuplot. If you install gnuplot via MacPorts though it will probably already take care of this dependency and install it for you... Cheers, Pi On Apr 24, 2011, at 3:57 AM, Whyte, Jeffrey wrote: Hi Pieter, Thanks very much for taking the time to provide the advice and explanations - very helpful! As you suggested, my search path was not defined properly to locate gnuplot. If I typed gnuplot in the Terminal, I would get the message, command not found. Now, Gnuplot is in /usr/local/bin and this directory is listed when I type echo $PATH. Now when I type gnuplot in the terminal, I get: $ gnuplot G N U P L O T Version 4.4 patchlevel 3 last modified March 2011 System: Darwin 10.7.0 Copyright (C) 1986-1993, 1998, 2004, 2007-2010 Thomas Williams, Colin Kelley and many others gnuplot home: http://www.gnuplot.info faq, bugs, etc: type help seeking-assistance immediate help: type help plot window: hit 'h' Terminal type set to 'aqua' gnuplot When I start up Galaxy, and try to run the Boxplot tool, I now get a different error: An error occurred running this job: gnuplot set term png size 2048,768 ^ line 0: unknown or ambiguous terminal type; type just 'set terminal' for a list gnuplot plot '/Users/JJWhyte/galaxy-dist/database/files/000/dataset_6.dat' using 1:7:11:12:9 with candlest I think this is related to the environment, as you explained in your second paragraph. I tried starting gnuplot from the Terminal first, then typing set term xterm, and then exiting, but this didn't change the error. Could you please explain how you set the environment in the galaxy/run.sh script? Again, I appreciate the help. Jeff On Apr 23, 2011, at 8:11 AM, Pieter Neerincx wrote: Hi Jeff, This is indeed a dependency issue and I have seen those both on Linux and Mac OS X. What happens if you type gnuplot in a Terminal window yourself? If you also get command not found. There is either still something missing or your environment is not setup properly. If the tool works if you execute it yourself in the Terminal, but it fails in Galaxy, you do have all the dependencies and it's clearly an environment setup issue: your OS will search for the binaries in a search path defined by the $PATH environment variable. This means that if you call gnuplot without specifying the path where it is installed, the OS will look in all directories specified in $PATH to find it. If it cannot find it, it will give you command not found. Additionally you may have
Re: [galaxy-dev] User Name not set with external LDAP authentication
Hi Leandro,
On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote:
Hi,
Just wondering if I got my setup right, I have Galaxy front-ended by Apache
doing the static caching, proxying and LDAP auth. What's nice is that user's
don't have to be created by an admin if the user authenticates and authorizes
properly against the LDAP config then Galaxy will automatically create the
user locally.
My question is that it shows that the User Name is not set for such users,
is this the way its supposed to be
No
or can I modify my LDAP config in such a way that it does set a User Name?
Yes, you can. I have a similar setup:
#
# For short logins. (Requires rewriting AuthLDAPBindDN to long form.)
#
AuthLDAPURL
ldap://ldap.uu.nl/ou=medewerkers,o=uu?uuShortID,uuMail;
AuthLDAPBindDN
uid=${REMOTE_USER}@soliscom.uu.nl,ou=medewerkers,o=uu
#
# Pass the user's e-mail address on to Galaxy as login
#
RewriteEngine On
RequestHeader set REMOTE_USER %{AUTHENTICATE_UUMAIL}e
Note that the uuMail attribute requested via the AuthLDAPURL somehow gets
expanded into an AUTHENTICATE_UUMAIL environment variable, which can then be
used to rewrite REMOTE_USER. You should be able to get something similar, but
the exact syntax will depend on the attributes defined in your LDAP. Note that
the example above allows my users to login with the part of their account
before the @. Since the domain part after the @ is the same for all of them
(soliscom.uu.nl), this saves them some typing when logging in :). Their e-mail
addresses may be different though, so I rewrite the REMOTE_USER to display
their e-mail address as Galaxy account in the web interface.
Cheers,
Pi
regards,
Leandro
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Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
Hi Jeff, On Apr 28, 2011, at 12:42 AM, Whyte, Jeffrey wrote: Hi Pieter, Thanks to both you and Florent for the suggestion of MacPorts. GnuPlot is now working well in Galaxy after I installed the port. :) I also appreciate the information on specifying the custom environment. That could be related to the only other problem I am having: the FASTX toolkit barcode splitter. Other FASTX tools like rename sequences and trim end work just fine, but the barcode splitter gives the following error in Galaxy: An error occurred running this job:sed: illegal option -- r usage: sed script [-Ealn] [-i extension] [file ...] Unfortunately, I don't believe there is a port of the FASTX tools available through MacPorts. I have gone through the instructions on the Hannon Lab webpage to try to install exactly as specified, but still get the error, although now at least Galaxy knows where to look to find the tools. I don't believe this is related to the PATH, as the error in Galaxy seems to relate to an option setting. That seems correct. I just checked sed on a Mac OS X laptop and a linux server: the one distributed with Mac OS X does not have a --r option whereas the one on Linux does. From man sed on linux: -r, --regexp-extended use extended regular expressions in the script. There is no -r in sed on Mac OS X, but from man sed: -E Interpret regular expressions as extended (modern) regular expressions rather than basic regular expressions (BRE's). The re_format(7) manual page fully describes both formats. Just from the description this -E option seems extremely similar if it isn't just plain the same, so you may try to change the sed -r command into sed -E in galaxy/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh If that doesn't work you either have to hack the code of this tool :o or try to install a compatible version of sed... Cheers, Pi I have run this barcode splitting on the public Galaxy server with no problems, and I simply used the same barcode definitions and joined file in my local instance of Galaxy, but get the error. I'll give you a break :) and keep working on it to see if I can trace the source of the error. Many thanks again, Jeff On Apr 27, 2011, at 4:10 AM, Pieter Neerincx wrote: Hi Jeff, 1. As Florent wrote, probably the easiest solution is to install the dependencies with MacPorts. Only if stuff is not available via MacPorts or the version available is too old / incompatible with other dependencies I install things manually. MacPorts will add a line like this: - export PATH=/opt/local/bin:/opt/local/sbin:$PATH - to your ~/.profile file, which is automatically sourced when you open a new Terminal window. Galaxy is probably running using a different account than yours. Usually a dedicated one or one used for the webserver like _www or www or apache or ... This user must have the same addition to it's environment in order to find gnuplot et al. To give Galaxy the same environment you can either add the line above to galaxy/run.sh immediately after the first line that identifies the file as a shell script (#!/bin/sh) and before the code that starts Galaxy. Optionally you may specify the environment in a separate file and source this file. Personally I like the latter, because I can manage the environment for multiple users and software packages in a single file that I can call from various locations. To source a file you use the . command. Hence [dot][space][path to env file]. Your galaxy/run.sh would start like this: - #!/bin/sh # # Source my custom environment including the path to MacPorts and other stuff I installed outside the default search paths # . /path/to/our_environment.bashrc - In our_environment.bashrc you would than have the same line: export PATH=/opt/local/bin:/opt/local/sbin:$PATH and potentially other stuff to set your environment. 2. For the gnuplot error below unknown or ambiguous terminal type: It seems the gnuplot script Galaxy is calling is trying to use an unsupported terminal. When you save the figure to a file a terminal is just a file type. In order to write jpeg, tiff, png, pdf, svg, etc. images gnuplot uses several libraries. When you install gnuplot it will look which libraries are available and based on that some image file formats may be available and others will not. It seems png support is not available. When you start a gnuplot terminal and type 'set terminal' for a list, do you see png as a supported terminal? If not, you should probably install libpng first and re-compile gnuplot. If you install gnuplot via MacPorts though it will probably already take care of this dependency and install it for you... Cheers, Pi On Apr 24, 2011
Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
Hi Jeff, This is indeed a dependency issue and I have seen those both on Linux and Mac OS X. What happens if you type gnuplot in a Terminal window yourself? If you also get command not found. There is either still something missing or your environment is not setup properly. If the tool works if you execute it yourself in the Terminal, but it fails in Galaxy, you do have all the dependencies and it's clearly an environment setup issue: your OS will search for the binaries in a search path defined by the $PATH environment variable. This means that if you call gnuplot without specifying the path where it is installed, the OS will look in all directories specified in $PATH to find it. If it cannot find it, it will give you command not found. Additionally you may have to set $LD_LIBRARY_PATH as well if the installed tools link to libraries installed outside default locations. Hence if you go to the Terminal and type: echo $PATH You will see a colon separated list of directories that should include the location where the gnuplot binary is installed. If this is not the case, please Google for setting $PATH on Mac OS X. If gnuplot does work if you execute it on the commandline, but it fails in Galaxy, it most likely means the environment for the user used to run Galaxy is different from yours (and the location where gnuplot is installed is missing from $PATH). In that case you can either set the environment in the galaxy/run.sh script used to start Galaxy or if you can call a bashrc script to set the environment from galaxy/run.sh. I use the latter where I have one bashrc script that sets the environment for all users and by calling this one from galaxy/run.sh I make sure the environment for Galaxy is exactly the same as for my (command line) users. Cheers, Pi On Apr 22, 2011, at 5:25 PM, Whyte, Jeffrey wrote: Hi Everyone, I'm having trouble getting some of the tools to work on my local installation of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy wiki are clear, and I was able to download and install from the anonymous Mercurial repository. Galaxy starts up and runs just fine for tools like Get Data, FASTQ Groomer, and FASTQ Summary Statistics. The problems started when I try to run Graph/Data Display - Boxplot (GnuPlot). I get the error: An error occurred running this job:/bin/sh: gnuplot: command not found Error running gnuplot. The FASTX Barcode Splitter also gives me an error: An error occurred running this job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file or directory sed: illegal opt I'm assuming these are Tool Dependency problems, although I have tried to install the OS X versions of GnuPlot and the FASTX Toolkit and still get errors. Are there any suggestions from users who are successfully running Galaxy on OS X? Thanks in advance, Jeff ___ 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Access control for galaxy
Hi Raghu, On Apr 21, 2011, at 4:44 AM, Raghuraman Ramamurthy wrote: Hello, I would first like to thank and appreciate the Galaxy team for their efforts. I want to clone galaxy and host it in my website. In doing so, I want to restrict the users who use galaxy on my website. So, is there any access control module which could be integrated with galaxy, to make it secure and grant access to only a set number of people. Have a look at External Authentication as described here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy Cheers, Pi Thanks, Raghu ___ 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/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ 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] Percent and pipe sign in text input fields
Hi Alex, Galaxy sanitizes the params to remove unsafe characters. It's a security feature. From a previous post some time ago: If you trust your users you can add the option name to NEVER_SANITIZE in lib/galaxy/utils/_init_.py You can also have a look at that *.py file and lib/galaxy/tools/parameters/sanitize.py to see what gets sanitized. AFAIK this is not well documented on the Wiki... Cheers, Pi On Feb 16, 2011, at 1:23 PM, Bossers, Alex wrote: Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Percent and pipe sign in text input fields
On Feb 16, 2011, at 3:44 PM, Pieter Neerincx wrote: Hi Alex, Galaxy sanitizes the params to remove unsafe characters. It's a security feature. From a previous post some time ago: If you trust your users you can add the option name to NEVER_SANITIZE in lib/galaxy/utils/_init_.py You can also have a look at that *.py file and lib/galaxy/tools/parameters/sanitize.py to see what gets sanitized. AFAIK this is not well documented on the Wiki... Eh, Google was not my friend, but it is actually documented: have a look at the sanititzer tag set... Cheers, Pi On Feb 16, 2011, at 1:23 PM, Bossers, Alex wrote: Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is XgXXaXXt. So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - - mobile: +31 6 143 66 783 e-mail: pieter.neeri...@gmail.com skype: pieter.online - ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
