Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week
Hi,
This issue is appearing again, after the upgrade of our Galaxy on October the
23rdanyone experiencing the same?
Thanks,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: vrijdag 4 april 2014 10:59
To: Bossers, Alex; Kuijt, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of
last week
Hi Alex, all
FYI - I've added the card to https://trello.com/c/ro8knsaa some time ago. Can
you please vote for it?
Thanks,
Pieter.
From: Bossers, Alex
Sent: dinsdag 25 maart 2014 16:52
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Strange issue with datatypes in Galaxy version of
last week
Pieter,
I just experienced the same with another generic tabular .tab file output. It
broke the filename at dash without any extension.
The file itself was ok, just the name.
Alex
Van:
galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Lukasse, Pieter
Verzonden: dinsdag 25 maart 2014 16:33
Aan: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] Strange issue with datatypes in Galaxy version of last
week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
datatype extension=msclust.csv type=galaxy.datatypes.tabular:Tabular
mimetype=text/csv display_in_upload=true subclass=true/
At first Galaxy output seems fine:
[cid:image001.png@01D003FF.9BD73320]
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to edit attributes and just click save, then upon downloading
again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
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Re: [galaxy-dev] Public toolshed giving internal server error
I am also having problems when using the option Search and browse toolsheds ! [cid:image001.jpg@01D0040B.AF3C7270] -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Briggs Sent: woensdag 19 november 2014 14:01 To: Björn Grüning; Galaxy Dev Subject: Re: [galaxy-dev] Public toolshed giving internal server error Hello Bjoern Thanks, seems to be okay now (on the main toolshed) - I can log out, log back in, and create and populate my new repository now. Thanks, best wishes Peter On 19/11/14 10:57, Björn Grüning wrote: Hi Peter, can you try again? I'm able to browse the ToolShed and reset metatada for example. Cheers, Bjoern Am 19.11.2014 um 10:36 schrieb Peter Briggs: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.ukmailto:peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] Tool shed environment dependency - HOW TO do this?
Indeed...painful and slow :( What I need is R 3.1.1 or later...so if I can get a pre-compiled package in toolshed that works I’m also happy! I understand Dave manages this process? @Dave: can you help me? Thanks, Pieter From: bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com] Sent: woensdag 12 november 2014 17:18 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Yes, this is correct. Do you really need to compile it by yourself? This is really a pain, I tried it during the R2 lifetime and this wasn't fun. 2014-11-12 17:10 GMT+01:00 Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl: Ok, I didn’t know that...but it does explain the behavior we are observing. So the actions_group tag is a kind of switch/try mechanism where the next applicable actions part is only executed if the previous one fails? Is that how I should read it? So my script is based on the last part, which actually tries to compile R with cairoand unfortunately this is not working. But maybe this was not detected by others because as you wrote, the compilation part is only a fall back (and probably will not be executed in practice)...? Thanks, Pieter. From: bjoern.gruen...@googlemail.commailto:bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.commailto:bjoern.gruen...@gmail.com] Sent: woensdag 12 november 2014 17:01 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Pieter, the compilation and hence the dependencies on the libraries for compilation are a fallback mechanism. This recipe will try to fetch binaries, if this does not work, or if the admin reconfigured Galaxy ... we try to compile R by our own. Hope this helps, Bjoern 2014-11-12 16:57 GMT+01:00 Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl: Hi Bjoern, Dave, I have been trying to understand how https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3 works . It contains a number of package dependencies as shown in the XML below. However, none show up in the toolshed UI (next screenshot). Is this because the package entries (libpng, cairo, etc) are inside a actions tag while they should be outside of this tag? Could it be these are not executed after all? Furthermore, the installation actually seems to be a simple download of a pre-compiled R version from depot.galaxy.orghttp://depot.galaxy.org . So why the ./configure and make commands further down the XML? Thanks for your help! Pieter -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.commailto:bjoern.gruen...@gmail.com] Sent: donderdag 30 oktober 2014 11:25 To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu; Lukasse, Pieter; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Pieter, Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter: Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the setup_r_environment trick. Why? Do you need a new release? The latest current release in the Tool Shed is R 3.1.0. If this is not enough we need to poke Dave to build a new package. But this way would be the preferred way. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor packagethe question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. If you really want to build your R packages by your own. Have a look at https://github.com/bgruening/galaxytools/blob/master/packages/package_r_3_0_3/tool_dependencies.xml You will find an exhaustive installation instruction how to build R properly. Also note that we export a variable called R_ROOT_DIR that is set to $INSTALL_DIR. You can now access R_ROOT_DIR from any other tool_dependency file ... Hope this helps, Bjoern P.S. Do you mind asking this question on biostar again, I think this is a very nice question that can be of interest to a lot more people. Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122tel:%2B31-317481122; M: +31-628189540tel:%2B31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/http://www.pri.wur.nl%3chttp:/www.pri.wur.nl
Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Ah, great! Please let me know once I can use it. Thanks, Pieter -Original Message- From: Dave Bouvier [mailto:d...@bx.psu.edu] Sent: woensdag 12 november 2014 17:27 To: Lukasse, Pieter; 'bjoern.gruen...@googlemail.com' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Pieter, I am in fact planning on compiling R 3.1.1 for depot.galaxyproject in the near future. --Dave B. On 11/12/2014 11:25 AM, Lukasse, Pieter wrote: Indeed...painful and slow :( What I need is R 3.1.1 or later...so if I can get a pre-compiled package in toolshed that works I’m also happy! I understand Dave manages this process? @Dave: can you help me? Thanks, Pieter *From:*bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com] *Sent:* woensdag 12 november 2014 17:18 *To:* Lukasse, Pieter *Cc:* galaxy-dev@lists.bx.psu.edu; Dave Bouvier *Subject:* Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Yes, this is correct. Do you really need to compile it by yourself? This is really a pain, I tried it during the R2 lifetime and this wasn't fun. 2014-11-12 17:10 GMT+01:00 Lukasse, Pieter pieter.luka...@wur.nl mailto:pieter.luka...@wur.nl: Ok, I didn’t know that...but it does explain the behavior we are observing. So the actions_group tag is a kind of switch/try mechanism where the next applicable actions part is only executed if the previous one fails? Is that how I should read it? So my script is based on the last part, which actually tries to compile R with cairoand unfortunately this is not working. But maybe this was not detected by others because as you wrote, the compilation part is only a fall back (and probably will not be executed in practice)...? Thanks, Pieter. *From:*bjoern.gruen...@googlemail.com mailto:bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com mailto:bjoern.gruen...@gmail.com] *Sent:* woensdag 12 november 2014 17:01 *To:* Lukasse, Pieter *Cc:* galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu; Dave Bouvier *Subject:* Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Pieter, the compilation and hence the dependencies on the libraries for compilation are a fallback mechanism. This recipe will try to fetch binaries, if this does not work, or if the admin reconfigured Galaxy ... we try to compile R by our own. Hope this helps, Bjoern 2014-11-12 16:57 GMT+01:00 Lukasse, Pieter pieter.luka...@wur.nl mailto:pieter.luka...@wur.nl: Hi Bjoern, Dave, I have been trying to understand how https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3 works . It contains a number of package dependencies as shown in the XML below. However, none show up in the toolshed UI (next screenshot). Is this because the package entries (libpng, cairo, etc) are inside a actions tag while they should be outside of this tag? Could it be these are not executed after all? Furthermore, the installation actually seems to be a simple download of a pre-compiled R version from depot.galaxy.org http://depot.galaxy.org . So why the ./configure and make commands further down the XML? Thanks for your help! Pieter -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com mailto:bjoern.gruen...@gmail.com] Sent: donderdag 30 oktober 2014 11:25 To: galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu; Lukasse, Pieter; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Pieter, Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter: Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the setup_r_environment trick. Why? Do you need a new release? The latest current release in the Tool Shed is R 3.1.0. If this is not enough we need to poke Dave to build a new package. But this way would be the preferred way. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor packagethe question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. If you really want to build your R packages by your own. Have a look at https://github.com/bgruening/galaxytools/blob/master/packages/package_ r_3_0_3/tool_dependencies.xml You will find an exhaustive installation instruction how to build R properly. Also note that we export a variable called R_ROOT_DIR that is set to $INSTALL_DIR. You can now access R_ROOT_DIR from any other tool_dependency file
Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Hi Bjoern, Thanks for this reply. I will have to try referring to the R_ROOT_DIR from another tool_dependency. If it doesn't work I'll come back ;) Regards, Pieter -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 30 oktober 2014 11:25 To: galaxy-dev@lists.bx.psu.edu; Lukasse, Pieter; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Pieter, Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter: Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the setup_r_environment trick. Why? Do you need a new release? The latest current release in the Tool Shed is R 3.1.0. If this is not enough we need to poke Dave to build a new package. But this way would be the preferred way. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor packagethe question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. If you really want to build your R packages by your own. Have a look at https://github.com/bgruening/galaxytools/blob/master/packages/package_r_3_0_3/tool_dependencies.xml You will find an exhaustive installation instruction how to build R properly. Also note that we export a variable called R_ROOT_DIR that is set to $INSTALL_DIR. You can now access R_ROOT_DIR from any other tool_dependency file ... Hope this helps, Bjoern P.S. Do you mind asking this question on biostar again, I think this is a very nice question that can be of interest to a lot more people. Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ 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] strange issue with .RData files
An alternative would be perhaps to look at the file name. If it ends in
“.RData” then I could mark it as such. Being able to access the original file
name (so not the internal one but the name that also appears in the history UI)
would allow me to do this. What would be the way to access this from within my
sniff method?
Thanks,
Pieter
From: Ross [mailto:ross.laza...@gmail.com]
Sent: donderdag 30 oktober 2014 11:20
To: Lukasse, Pieter
Cc: John Chilton; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
Rdata is binary and serialises R objects so I sure hope you don't have to peek
inside - probably needs most of an R environment - like rpy or something.
A binary header signature magic number would be ideal - I checked a few saved
rdata files lying around here and all seemed to start with the following bytes
- all were variable after the 12th:
1f 8b 08 00 00 00 00 00 00 03 d4 fd
Maybe someone else can confirm that as a reliable binary hex header signature
for rdata?
I couldn't find anything in the R docs - probably take a good deep dive into
the guts of the save/load function source to be sure.
On Thu, Oct 30, 2014 at 8:54 PM, Lukasse, Pieter
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote:
Hi John,
Yes, I think this should work as I have seen it work for another binary type I
made before. See below:
class FileSet( Binary ):
FileSet containing N files
file_ext = prims.fileset.zip
blurb = (zipped) FileSet containing multiple files
def sniff( self, filename ):
# If the zip file contains multiple files then return true, false
otherwise:
zf = zipfile.ZipFile(filename)
if (len(zf.infolist())1):
return True
else :
return False
# the if is just for backwards compatibility...could remove this at some point
if hasattr(Binary, 'register_sniffable_binary_format'):
Binary.register_sniffable_binary_format('FileSet', 'prims.fileset.zip',
FileSet)
Now the question I have is: what would be a good logic to use in the sniff
method? I need something that uniquely distinguishes this zipped file from
other zip files, right? In the previous example above I found a solution by
checking whether the zip file has multiple files inside and return true if this
is the case. Now with RData, does it mean I have to try to parse the binary
contents inside and come with a good heuristic/rule ? Just wondering if someone
already has thought about such a rule, specifically for RData.
Thanks,
Pieter.
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.commailto:jmchil...@gmail.com]
Sent: donderdag 23 oktober 2014 3:02
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
Hey Pieter,
Sorry I am swamped right now so I don't have time to dig into this in detail
- but I have encountered this before with datatypes that are compressed -
zipped, gzipped, etc Galaxy will attempt to decompress them in order to
figure out what they are. I believe this is what is happening to your data. If
you register the type as a sniffable binary it looks like it should skip the
decompression though
- unless I am reading this logic wrong in tools/data_source/upload.py
https://gist.github.com/jmchilton/54b5d7485fcd16eec984.
E.g. like bam datatypes:
class Bam( Binary ):
Binary.register_sniffable_binary_format(bam, bam, Bam)
Have you registered a sniffable binary datatype for RData?
-John
On Wed, Oct 22, 2014 at 9:38 AM, Lukasse, Pieter
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote:
Hi,
When I upload any .RData file to my Galaxy server it seems to be
unpacking/changing it. The resulting file in my history is different
and around 2x larger than the uploaded file. The tool that needs to
use it also aborts with an error due to this erroneous file.
What are the workarounds?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
http://www.pri.wur.nl
___
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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/
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http
Re: [galaxy-dev] strange issue with .RData files
Hi Ross,
I also found the following information:
“save works by writing a single-line header (typically RDX2\n for a binary
save: the only other current value is RDA2\n for save(files=TRUE)),”
From http://cran.r-project.org/doc/manuals/r-release/R-ints.html (section 1.8
– Serialization Formats).
Regards,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 november 2014 10:25
To: 'Ross'
Cc: John Chilton; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
An alternative would be perhaps to look at the file name. If it ends in
“.RData” then I could mark it as such. Being able to access the original file
name (so not the internal one but the name that also appears in the history UI)
would allow me to do this. What would be the way to access this from within my
sniff method?
Thanks,
Pieter
From: Ross [mailto:ross.laza...@gmail.com]
Sent: donderdag 30 oktober 2014 11:20
To: Lukasse, Pieter
Cc: John Chilton;
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
Rdata is binary and serialises R objects so I sure hope you don't have to peek
inside - probably needs most of an R environment - like rpy or something.
A binary header signature magic number would be ideal - I checked a few saved
rdata files lying around here and all seemed to start with the following bytes
- all were variable after the 12th:
1f 8b 08 00 00 00 00 00 00 03 d4 fd
Maybe someone else can confirm that as a reliable binary hex header signature
for rdata?
I couldn't find anything in the R docs - probably take a good deep dive into
the guts of the save/load function source to be sure.
On Thu, Oct 30, 2014 at 8:54 PM, Lukasse, Pieter
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote:
Hi John,
Yes, I think this should work as I have seen it work for another binary type I
made before. See below:
class FileSet( Binary ):
FileSet containing N files
file_ext = prims.fileset.zip
blurb = (zipped) FileSet containing multiple files
def sniff( self, filename ):
# If the zip file contains multiple files then return true, false
otherwise:
zf = zipfile.ZipFile(filename)
if (len(zf.infolist())1):
return True
else :
return False
# the if is just for backwards compatibility...could remove this at some point
if hasattr(Binary, 'register_sniffable_binary_format'):
Binary.register_sniffable_binary_format('FileSet', 'prims.fileset.zip',
FileSet)
Now the question I have is: what would be a good logic to use in the sniff
method? I need something that uniquely distinguishes this zipped file from
other zip files, right? In the previous example above I found a solution by
checking whether the zip file has multiple files inside and return true if this
is the case. Now with RData, does it mean I have to try to parse the binary
contents inside and come with a good heuristic/rule ? Just wondering if someone
already has thought about such a rule, specifically for RData.
Thanks,
Pieter.
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.commailto:jmchil...@gmail.com]
Sent: donderdag 23 oktober 2014 3:02
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
Hey Pieter,
Sorry I am swamped right now so I don't have time to dig into this in detail
- but I have encountered this before with datatypes that are compressed -
zipped, gzipped, etc Galaxy will attempt to decompress them in order to
figure out what they are. I believe this is what is happening to your data. If
you register the type as a sniffable binary it looks like it should skip the
decompression though
- unless I am reading this logic wrong in tools/data_source/upload.py
https://gist.github.com/jmchilton/54b5d7485fcd16eec984.
E.g. like bam datatypes:
class Bam( Binary ):
Binary.register_sniffable_binary_format(bam, bam, Bam)
Have you registered a sniffable binary datatype for RData?
-John
On Wed, Oct 22, 2014 at 9:38 AM, Lukasse, Pieter
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote:
Hi,
When I upload any .RData file to my Galaxy server it seems to be
unpacking/changing it. The resulting file in my history is different
and around 2x larger than the uploaded file. The tool that needs to
use it also aborts with an error due to this erroneous file.
What are the workarounds?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
http://www.pri.wur.nl
___
Please
Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Hi Bjoern, I tried your suggestion, but it didn't work. So now I have split up the R part from the Bioconductor part (blue and yellow below, respectively). But the problem is that the install part executes before the package part is finished and the $R_ROOT_DIR reference also doesn't seem to work as I get the following error : /bin/sh: 1: /bin/Rscript: not found . This R_ROOT_DIR is set by the package script in my other tool_dependency.xml but is not visible in the tool_dependency.xml below. But maybe I misunderstood what you meant by You can now access R_ROOT_DIR from any other tool_dependency file ...? tool_dependency !-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help -- package name=R_bioc_metams version=3.1.1 repository changeset_revision=0af753942e7b name=prims_metabolomics_dependencies owner=pieterlukasse prior_installation_required=True toolshed=http://testtoolshed.g2.bx.psu.edu; / install version=1.0 actions_group !-- the Bioconductor and metaMS part -- action type=shell_commandwget -P $INSTALL_DIR http://testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics/raw-file/tip/INSTALL.r/action action type=shell_command$R_ROOT_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r/action /actions_group /install /package readme This dependency: Ensures R 3.1.1 installation is triggered (via dependency). Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. /readme /tool_dependency Thanks, Pieter -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 6 november 2014 10:02 To: 'Björn Grüning'; galaxy-dev@lists.bx.psu.edu; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Bjoern, Thanks for this reply. I will have to try referring to the R_ROOT_DIR from another tool_dependency. If it doesn't work I'll come back ;) Regards, Pieter -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 30 oktober 2014 11:25 To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu; Lukasse, Pieter; Dave Bouvier Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this? Hi Pieter, Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter: Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the setup_r_environment trick. Why? Do you need a new release? The latest current release in the Tool Shed is R 3.1.0. If this is not enough we need to poke Dave to build a new package. But this way would be the preferred way. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor packagethe question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. If you really want to build your R packages by your own. Have a look at https://github.com/bgruening/galaxytools/blob/master/packages/package_r_3_0_3/tool_dependencies.xml You will find an exhaustive installation instruction how to build R properly. Also note that we export a variable called R_ROOT_DIR that is set to $INSTALL_DIR. You can now access R_ROOT_DIR from any other tool_dependency file ... Hope this helps, Bjoern P.S. Do you mind asking this question on biostar again, I think this is a very nice question that can be of interest to a lot more people. Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/http://www.pri.wur.nl%3chttp:/www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies
Re: [galaxy-dev] strange issue with .RData files
Hi John,
Yes, I think this should work as I have seen it work for another binary type I
made before. See below:
class FileSet( Binary ):
FileSet containing N files
file_ext = prims.fileset.zip
blurb = (zipped) FileSet containing multiple files
def sniff( self, filename ):
# If the zip file contains multiple files then return true, false
otherwise:
zf = zipfile.ZipFile(filename)
if (len(zf.infolist())1):
return True
else :
return False
# the if is just for backwards compatibility...could remove this at some point
if hasattr(Binary, 'register_sniffable_binary_format'):
Binary.register_sniffable_binary_format('FileSet', 'prims.fileset.zip',
FileSet)
Now the question I have is: what would be a good logic to use in the sniff
method? I need something that uniquely distinguishes this zipped file from
other zip files, right? In the previous example above I found a solution by
checking whether the zip file has multiple files inside and return true if this
is the case. Now with RData, does it mean I have to try to parse the binary
contents inside and come with a good heuristic/rule ? Just wondering if someone
already has thought about such a rule, specifically for RData.
Thanks,
Pieter.
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: donderdag 23 oktober 2014 3:02
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
Hey Pieter,
Sorry I am swamped right now so I don't have time to dig into this in detail
- but I have encountered this before with datatypes that are compressed -
zipped, gzipped, etc Galaxy will attempt to decompress them in order to
figure out what they are. I believe this is what is happening to your data. If
you register the type as a sniffable binary it looks like it should skip the
decompression though
- unless I am reading this logic wrong in tools/data_source/upload.py
https://gist.github.com/jmchilton/54b5d7485fcd16eec984.
E.g. like bam datatypes:
class Bam( Binary ):
Binary.register_sniffable_binary_format(bam, bam, Bam)
Have you registered a sniffable binary datatype for RData?
-John
On Wed, Oct 22, 2014 at 9:38 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote:
Hi,
When I upload any .RData file to my Galaxy server it seems to be
unpacking/changing it. The resulting file in my history is different
and around 2x larger than the uploaded file. The tool that needs to
use it also aborts with an error due to this erroneous file.
What are the workarounds?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
http://www.pri.wur.nl
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[galaxy-dev] Tool shed environment dependency - HOW TO do this?
Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the setup_r_environment trick. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor packagethe question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ ?xml version=1.0? tool_dependency !-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help partly based on : https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3 -- package name=R_bioc_metams version=3.1.1 install version=1.0 actions_group actions action type=download_by_urlhttp://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz/action action type=move_directory_files source_directory./source_directory destination_directory$INSTALL_DIR/destination_directory /action action type=shell_command cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR /action action type=shell_commandmake -C $INSTALL_DIR/action /actions action type=set_environment environment_variable action=set_to name=R_DOC_DIR$INSTALL_DIR/doc/environment_variable environment_variable action=set_to name=R_HOME_DIR$INSTALL_DIR/environment_variable environment_variable action=set_to name=R_INCLUDE_DIR$INSTALL_DIR/include/environment_variable environment_variable action=set_to name=R_SHARE_DIR$INSTALL_DIR/share/environment_variable environment_variable action=set_to name=R_ROOT_DIR$INSTALL_DIR/environment_variable environment_variable action=set_to name=R_HOME$INSTALL_DIR/environment_variable environment_variable action=set_to name=RHOME$INSTALL_DIR/environment_variable environment_variable action=set_to name=R_LIBS$INSTALL_DIR/library/environment_variable environment_variable action=prepend_to name=PATH$INSTALL_DIR/bin/environment_variable /action !-- the Bioconductor and metaMS part -- action type=shell_commandwget -P $INSTALL_DIR http://testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_dependencies/raw-file/tip/INSTALL.r/action action type=shell_command$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r/action /actions_group /install readme Ensures R 3.1.1 is installed. Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. R is a free software environment for statistical computing and graphics. /readme /package /tool_dependency___ 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] Dependencies not working on toolshed?
Hi Bjoern, John, thanks, this worked! So: I have to add a repository dependency to my tool_dependencies.xml file and NOT to my repository_dependencies.xmlI must say it is somewhat confusing. Somehow I had this idea that tool_dependencies.xml was for external tools But I'm happy it finally works! Thanks again, Pieter. -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: vrijdag 24 oktober 2014 16:23 To: Lukasse, Pieter; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Dependencies not working on toolshed? Pieter, please try to add your dependencies to a tool_dependencies.xml file not the repository_dependencies.xml file. repository_dependencies.xml is for datatypes and for workflow dependencies, such things that need to be there, but that are not referenced from the tool. Hope this helps, Bjoern Am 24.10.2014 um 16:18 schrieb Lukasse, Pieter: Hi , I am trying to get a dependency to work in practice (when running a tool after the installation). But I keep getting the following message when running the tool: [sshexec] galaxy.tools.deps DEBUG 2014-10-24 16:04:15,514 Building dependency shell command for dependency 'R_bioc_metams' [sshexec] galaxy.tools.deps WARNING 2014-10-24 16:04:15,514 Failed to resolve dependency on 'R_bioc_metams', ignoring This is the tool requirements section: requirements requirement type=package version=3.1.1R_bioc_metams/requirement /requirements This is the repository_dependencies.xml : repositories description=Required metaMS dependencies. repository toolshed=http://testtoolshed.g2.bx.psu.edu; name=prims_metabolomics_dependencies owner=pieterlukasse changeset_revision=71356c62e5cd / /repositories This is the package name of the package that is being referred: tool_dependency package name=R_bioc_metams version=3.1.1 install version=1.0 actions_group I can't find the problem. Any ideas? I have updated to the latest Galaxy version (today) and removed both items (with option to remove files) and installed them again. Am I facing a bug here? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ 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/
[galaxy-dev] Dependencies not working on toolshed?
Hi , I am trying to get a dependency to work in practice (when running a tool after the installation). But I keep getting the following message when running the tool: [sshexec] galaxy.tools.deps DEBUG 2014-10-24 16:04:15,514 Building dependency shell command for dependency 'R_bioc_metams' [sshexec] galaxy.tools.deps WARNING 2014-10-24 16:04:15,514 Failed to resolve dependency on 'R_bioc_metams', ignoring This is the tool requirements section: requirements requirement type=package version=3.1.1R_bioc_metams/requirement /requirements This is the repository_dependencies.xml : repositories description=Required metaMS dependencies. repository toolshed=http://testtoolshed.g2.bx.psu.edu; name=prims_metabolomics_dependencies owner=pieterlukasse changeset_revision=71356c62e5cd / /repositories This is the package name of the package that is being referred: tool_dependency package name=R_bioc_metams version=3.1.1 install version=1.0 actions_group I can't find the problem. Any ideas? I have updated to the latest Galaxy version (today) and removed both items (with option to remove files) and installed them again. Am I facing a bug here? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Citations tag not working
I can confirm it worked on my server as well (recent release) From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of John Chilton [jmchil...@gmail.com] Sent: Friday, October 24, 2014 3:57 PM To: James Mullan Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Citations tag not working This feature was added with the August 2014 release and it looks like you are still on the June release (latest_2014.06.02). You will need to upgrade to the August or October release (remember to run tool migrations). (This feature touched a number of different components and so I don't have a small patch I can give you for enabling it.) Here is the dev news release for the Augustus release: https://wiki.galaxyproject.org/DevNewsBriefs/2014_08_11 We still haven't released news for the October release but the upgrade process is similar and we have been running the October release on usegalaxy.org for over a month now. -John On Fri, Oct 24, 2014 at 9:29 AM, James Mullan jamespamul...@gmail.com wrote: Hello, I downloaded Galaxy a few months ago but I just noticed that the citations tag doesn't work on my download. The info on the hg pull I have is: hg tip changeset: 13771:7a4d321c0e38 branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Wed Jul 30 11:13:20 2014 -0400 summary: Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae What would I need to do if I wanted to include this functionality ? Regards jamesp J ames Mullan ___ 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/ ___ 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] filtering a param of type 'data' so only one type is available
Struggling with this now...you have my vote! From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ross Sent: donderdag 24 januari 2013 1:04 To: Dan Tenenbaum Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] filtering a param of type 'data' so only one type is available Hi, Dan Glad it worked and thanks for pointing out a more general mimetype - does any one else (other than me) want to vote to add datatype extension=rda type=galaxy.datatypes.binary:Binary mimetype=application/x-gzip subclass=True / to datatypes_conf.xml.sample permanently ? On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum dtene...@fhcrc.orgmailto:dtene...@fhcrc.org wrote: On Wed, Jan 23, 2013 at 3:51 PM, Ross ross.laza...@gmail.commailto:ross.laza...@gmail.com wrote: Hi, Dan. Using format=rda will restrict the list to history items of the 'rda' datatype - but ONLY if the rda datatype has been defined! The easiest way to do that is to define a new datatype in datatypes_conf.xml and since rData is binary, you should subclass binary. Something like (untested - especially the mimetype !) datatype extension=rda type=galaxy.datatypes.binary:Binary mimetype=application/x-rlang-transport subclass=True / might work. A server restart is always required to load any new datatypes. Good luck! It works! I changed the mime type to application/x-gzip, since serialized R objects are gzipped. Thanks, Dan On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum dtene...@fhcrc.orgmailto:dtene...@fhcrc.org wrote: Hi, I have a tool wrapper with a param of type=data. Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format=rda and that didn't seem to change anything. 2) rda is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan ___ 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] strange issue with .RData files
Hi, When I upload any .RData file to my Galaxy server it seems to be unpacking/changing it. The resulting file in my history is different and around 2x larger than the uploaded file. The tool that needs to use it also aborts with an error due to this erroneous file. What are the workarounds? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] HOWTO share tool parameter settings?
Hi John, I see that in my last email I replied to you with the fourth (and not the third) option in mind :(. Just to come back to this related to the third option (i.e. Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool): I don't like this option so much because the file is never as clear as the tool form that produced it. If users are used to looking at the tool form for seeing details about the set parameters and now they will have to look at a text file, this will be confusing. It is not a huge problem, but it is one that I am trying to avoid. I.e. it would be best if users are presented with only one way of checking parameters of executed processes. In the scenario I am proposing, the settings files are disseminated just as they are (e.g. a text file) either by sharing them in the normal ways or by placing a number of them in pre-defined folders in Galaxy. The tool form would allow the user to select one and would then fill in the values of the parameters accordingly. I'm guessing similar binding logic is also happening right now when a user clicks rerun on a step in his history. Best regards, Pieter. -Original Message- From: John Chilton [mailto:jmchil...@gmail.com] Sent: donderdag 9 oktober 2014 15:45 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] HOWTO share tool parameter settings? How would this be different then the third option you listed? You want it to work with all tools and you as the developer want to be able to construct these files without needing a dummy tool to produce the values? How would imagine these setting files would be disseminated to users and then selected by users? -John On Thu, Oct 9, 2014 at 9:34 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi, Do we have a way (or plans) for sharing tool parameter settings in Galaxy? I know the following workarounds : · Share a history with all users: so users can import your step and do “rerun” to run on their own file with your settings · Wrap the step in a workflow with all parameters set and publish this workflow: users can run this “workflow” · Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool · Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.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/ 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] HOWTO share tool parameter settings?
Hi John, The difference with an external settings-only file and the third option is that the last one has settings and layout mixed up. Say we want to change the order of two fields in a form, then with the macros approach I would need to change N macro files for N different versions (each version related to different set of parameter values). I could use the token option if it would allow for conditionally loading a different sets of token values, depending of e.g. a select box option by the user. I hope it is somewhat clearer now, but do not hesitate to send me more questions! Best regards, Pieter. -Original Message- From: John Chilton [mailto:jmchil...@gmail.com] Sent: donderdag 9 oktober 2014 15:45 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] HOWTO share tool parameter settings? How would this be different then the third option you listed? You want it to work with all tools and you as the developer want to be able to construct these files without needing a dummy tool to produce the values? How would imagine these setting files would be disseminated to users and then selected by users? -John On Thu, Oct 9, 2014 at 9:34 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi, Do we have a way (or plans) for sharing tool parameter settings in Galaxy? I know the following workarounds : · Share a history with all users: so users can import your step and do “rerun” to run on their own file with your settings · Wrap the step in a workflow with all parameters set and publish this workflow: users can run this “workflow” · Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool · Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.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/ 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/
[galaxy-dev] HOWTO share tool parameter settings?
Hi, Do we have a way (or plans) for sharing tool parameter settings in Galaxy? I know the following workarounds : * Share a history with all users: so users can import your step and do rerun to run on their own file with your settings * Wrap the step in a workflow with all parameters set and publish this workflow: users can run this workflow * Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool * Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] IE 11 issues
Hi Carl, Any news on this? Thanks, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Carl Eberhard Sent: dinsdag 29 juli 2014 16:35 To: Sajdak, Doris Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] IE 11 issues That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using either Chrome/Firefox or an older version of IE (10?). You might also try using IE's compatibility mode but this must be set on a per browser basis and might be tedious: https://kb.wisc.edu/page.php?id=35591 I'll update when I find out more and thanks for the report, Carl On Mon, Jul 28, 2014 at 1:24 PM, Sajdak, Doris dj...@buffalo.edumailto:dj...@buffalo.edu wrote: Hi Carl, Thanks for the help. Here’s what I get when I try to upload a new file: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: '$' is undefined File: tool_runner, Line: 64, Column: 13 SCRIPT5007: Unable to get property 'extend' of undefined or null reference File: galaxy.panels.js, Line: 28, Column: 1 SCRIPT5002: Function expected File: tool_runner, Line: 80, Column: 5 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 SCRIPT5002: Function expected File: galaxy.tools.js, Line: 9, Column: 5 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 I get the following when I click on the edit button next to one of the items in my history: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: 'jQuery' is undefined File: jquery.autocomplete.js, Line: 9, Column: 2 SCRIPT5009: 'jQuery' is undefined File: galaxy.autocom_tagging.js, Line: 20, Column: 1 SCRIPT5009: '$' is undefined File: edit, Line: 528, Column: 9 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 This is what I get from ‘hg summary:’ parent: 12442:29ce93a13ac7 tip Merge stable branch. branch: default commit: 1 modified, 177 unknown update: (current) Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s something wrong on my end. Thanks, Dori From: Carl Eberhard [mailto:carlfeberh...@gmail.commailto:carlfeberh...@gmail.com] Sent: Monday, July 28, 2014 10:55 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu; Sajdak, Doris Subject: Re: [galaxy-dev] IE 11 issues Hi, Dori Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs in the history panel now, but in the meantime: - can you open the javascript console in your IE and see if any errors are displayed when doing the two tasks you mention? http://msdn.microsoft.com/en-us/library/ie/bg182326%28v=vs.85%29.aspx - What version of Galaxy does your lab use currently? (You can view the version by using the 'hg summary' command from the directory from which Galaxy is run) As an aside, IE has traditionally veered away from web standards and made it difficult to program compatible sites. Recent versions of IE have become much more standards compliant allowing us to support them well enough. Please don't hesitate to report IE (10+) bugs when using Galaxy. Thanks for the report and I'll update with my findings soon, Carl On Mon, Jul 28, 2014 at 10:42 AM, Björn Grüning bjoern.gruen...@gmail.commailto:bjoern.gruen...@gmail.com wrote: Hi Dori, the IE is not really supported. There are many issues with IE and it's hard to deal with that. If possible please you Chrome or FF, both are supported and tested. Cheers, Bjoern Am 28.07.2014 um 16:40 schrieb Sajdak, Doris: We are having issues with using Galaxy in Internet Explorer 11 (these work fine in Chrome Firefox). 1. The jobs queued and history doesn't display unless you refresh the browser window. Clicking the history
Re: [galaxy-dev] IE 11 issues
Hi Dannon, Thanks for the info. We will test it on our server. Our last update seems to be from June 5th. Best regards, Pieter. From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: vrijdag 19 september 2014 12:29 To: Lukasse, Pieter Cc: Carl Eberhard; Sajdak, Doris; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] IE 11 issues Hi Pieter, I updated the jQuery library that ships with galaxy in revision 14425:068fa60b8c2b on August 19, which should hopefully have resolved these issues. Are you still seeing problems on a galaxy server updated past that revision? -Dannon On Fri, Sep 19, 2014 at 4:45 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi Carl, Any news on this? Thanks, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Carl Eberhard Sent: dinsdag 29 juli 2014 16:35 To: Sajdak, Doris Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] IE 11 issues That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using either Chrome/Firefox or an older version of IE (10?). You might also try using IE's compatibility mode but this must be set on a per browser basis and might be tedious: https://kb.wisc.edu/page.php?id=35591 I'll update when I find out more and thanks for the report, Carl On Mon, Jul 28, 2014 at 1:24 PM, Sajdak, Doris dj...@buffalo.edumailto:dj...@buffalo.edu wrote: Hi Carl, Thanks for the help. Here’s what I get when I try to upload a new file: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: '$' is undefined File: tool_runner, Line: 64, Column: 13 SCRIPT5007: Unable to get property 'extend' of undefined or null reference File: galaxy.panels.js, Line: 28, Column: 1 SCRIPT5002: Function expected File: tool_runner, Line: 80, Column: 5 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 SCRIPT5002: Function expected File: galaxy.tools.js, Line: 9, Column: 5 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 I get the following when I click on the edit button next to one of the items in my history: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: 'jQuery' is undefined File: jquery.autocomplete.js, Line: 9, Column: 2 SCRIPT5009: 'jQuery' is undefined File: galaxy.autocom_tagging.js, Line: 20, Column: 1 SCRIPT5009: '$' is undefined File: edit, Line: 528, Column: 9 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 This is what I get from ‘hg summary:’ parent: 12442:29ce93a13ac7 tip Merge stable branch. branch: default commit: 1 modified, 177 unknown update: (current) Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s something wrong on my end. Thanks, Dori From: Carl Eberhard [mailto:carlfeberh...@gmail.commailto:carlfeberh...@gmail.com] Sent: Monday, July 28, 2014 10:55 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu; Sajdak, Doris Subject: Re: [galaxy-dev] IE 11 issues Hi, Dori Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs in the history panel now, but in the meantime: - can you open the javascript console in your IE and see if any errors are displayed when doing the two tasks you mention? http://msdn.microsoft.com/en-us/library/ie/bg182326%28v=vs.85%29.aspx - What version of Galaxy does your lab use currently? (You can view the version by using the 'hg summary' command from the directory from which Galaxy is run) As an aside, IE has traditionally veered away from web standards and made it difficult to program compatible
Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that install and run JAR files properly?
Hi Melissa, Just commenting on point 1 of your email: did you try the “Reset metadata “ option? See screenshot below: [cid:image001.jpg@01CFC756.F193E4B0] For points 2 and 3: I normally look at the status (Installed/Green) and test whether the correct version appear in the menu for the users. I tend to ignore other messages or temporary(?)hiccups in the installation process web page. Regards, Pieter. From: melissa.s.cl...@gmail.com [mailto:melissa.s.cl...@gmail.com] On Behalf Of Melissa Cline Sent: woensdag 3 september 2014 3:23 To: Dave Bouvier Cc: Lukasse, Pieter; Peter Cock; Galaxy Dev Subject: Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that install and run JAR files properly? Peter, Pieter and Dave, thank you for the pointers to your tools - they've been extremely helpful! Now I can see how the process is supposed to work. I'm not really sure where mine is going wrong, but maybe someone here will have ideas. So folks, I've had partial success with a repository that includes a tool_dependencies.xml, which sets two environment variables and moves a JAR file from REPOSITORY_INSTALL_DIR to INSTALL_DIR. But the following things suggest to me that it's only a partial success, and I'm very interested in any insights to clear them up. 1. I have my repository checked into an internal tool shed. Somewhere in the course of development, I specified a buggy dependency, and now I can't seem to clear it up. When I go to (re)install my tool from the tool shed, here's what I see in the way of dependencies: Tool dependencies - these dependencies may not be required by tools in this repository Name Version Type Orphan JAR_PAHT set_environment yes and as you might imagine, I've checked the obvious things, and there is no more reference to JAR_PAHT (typos and all) anywhere in or around my tool, or in my galaxy-dist directory. It seems like there's some old metadata cruft that hasn't been cleared out. How can I clear it out? 2. When I install my tool, I see the following messages in paster.log: --- tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2014-09-02 17:13:59,279 Building repository dependency relationships... 172.30.0.22 - - [02/Sep/2014:17:13:59 -0700] POST /admin_toolshed/prepare_for_install HTTP/1.1 200 - http://tcga1:1235/admin_toolshed/prepare_for_install?tool_shed_url=http://medbook.ucsc.edu:9009/repository_ids=decab5ee1e95b10bchangeset_revisions=ff9b02e50bcf; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.143 Safari/537.36 172.30.0.22 - - [02/Sep/2014:17:14:02 -0700] POST /admin_toolshed/repository_installation_status_updates HTTP/1.1 200 - http://tcga1:1235/admin_toolshed/prepare_for_install; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.143 Safari/537.36 tool_shed.util.shed_util_common DEBUG 2014-09-02 17:14:03,477 Error attempting to get tool shed status for installed repository start_xena: HTTP Error 404: Not Found Attempting older 'check_for_updates' method. --- Should I be concerned about these last messages? I don't remember seeing them with Peter, Pieter and Dave's tools. 3. After my tool has installed, there is no INSTALLATION.log in my INSTALL_DIR. Does this mean that the installation process somehow terminated early? There is an env.sh file, with the correct values of the environment variables I'm setting in my tool_dependencies.xml, and my jar file is copied to INSTALL_DIR. In my Galaxy window, my tool is indicated as Installed, in green. Here are the last messages I see in paster.log: tool_shed.galaxy_install.install_manager DEBUG 2014-09-02 17:14:04,630 Changing status for tool dependency installXena from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2014-09-02 17:14:04,669 Tool dependency installXena version 1.0 has been installed in /inside/home/cline/src/galaxy-dist/tool_dependencies/installXena/1.0/melissacline/start_xena/3e4683c94d8d. 172.30.0.22 - - [02/Sep/2014:17:13:59 -0700] POST /admin_toolshed/manage_repositories HTTP/1.1 302 - http://tcga1:1235/admin_toolshed/prepare_for_install; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.143 Safari/537.36 172.30.0.22 - - [02/Sep/2014:17:14:04 -0700] GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=3f5830403180d620 HTTP/1.1 200 - http://tcga1:1235/admin_toolshed/prepare_for_install; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.143 Safari/537.36 172.30.0.22 - - [02/Sep/2014:17:14:05 -0700] POST /admin_toolshed/repository_installation_status_updates HTTP/1.1 200 - http://tcga1:1235/admin_toolshed/prepare_for_install; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.143 Safari
Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that install and run JAR files properly?
Hi Melissa, See also https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb or https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_proteomics Regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock Sent: zaterdag 30 augustus 2014 4:32 To: Melissa Cline Cc: Galaxy Dev Subject: Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that install and run JAR files properly? On Sat, Aug 30, 2014 at 11:17 AM, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, I'm attempting something that should be straightforward, but it's not. I have a tool that runs a JAR file, which I have bundled with the tool. I simply want to run the JAR file. And to paraphrase Thomas Edison, I've tried several thousand things that do not work (at least for me), from setting the JAVA_JAR_PATH environment variable in the tool_dependencies.xml file to trying to copy the JAR file into the tool-data/shared/jars subdirectories (which is the closest thing I've got to working). So, at long last I'm doing the sensible thing and looking for one simple working example that I can use as a template. Who can suggest a good toolshed tool (either main or test) that involves running its own JAR file, and that works? Thanks! Melissa Here are a couple of my wrappers for Java tools, but I would suggest you invoke the Java script with an absolute path to the JAR file: $ java -jar ... Here is two examples done via a Python wrapper script (mainly used for pre or post processing the data files): https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go For EffectiveT3 which is open source and can therefore be easily redistributed, I set an environment variable EFFECTIVET3 for the location of the Jar file, which is used to invoke it via Java: $ java -jar ... For the Blast2GO wrapper, I require the person installing it setup an environment variable B2G4PIPE pointing at the folder with the JAR file. Older versions of this tool you be launched with the same -jar approach, but the current release requires setting a class path instead: $ java -cp ... I hope that helps, if not there are bound to be other Java examples in the ToolShed. 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/ 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] when else in conditional ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??
Yes, adding a when else option would be nice. However, what I really would like to have is a way to tell in one select box which other select box(es) should be refreshed when its value is changed by the user. For example: param name=cmb_col_type type=select label=Select column type param_to_refresh_on_change=cmb_polarity display=radio dynamic_options='get_column_type(library_file)' help= / param name=cmb_polarity type=select label=Select polarity display=radio dynamic_options='filter_column(library_file,cmb_col_type)' help= / So when cmb_col_type is changed, the dynamic_options of cmb_polarity are generated again by a new call to the function configured. I can create a Trello card, but I’m just wondering whether this is not already being planned by the team, especially with the Javascript/AJAX rework that is now planned/going on(?) for some time on the user interface? Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: zaterdag 30 augustus 2014 0:58 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] when else in conditional ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options?? On Fri, Aug 29, 2014 at 11:43 PM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: So I need to refresh on changeI see that if I have a conditional item in my form, this causes a refresh of the page and a (re)evaluation of my dynamic_options methodsso I could misuse this “feature”. This is deliberate, although there has been talk of updating the conditional code to do the dependent parameters dynamically rather than server-side with a page refresh. From your outline description, I think you should be using the Galaxy conditional tag. However, it seems that when I have a conditional I must have a when entry for every item in my select box. There is no “when else” option? I think you are right - I've asked in the past about this, e.g. this discussion which appears not to have been fully on the mailing list though: http://dev.list.galaxyproject.org/Multiple-values-in-lt-when-gt-tags-for-lt-conditiona-gt-parameters-tc4659704.html#none This probably deserves to be tracked with a Trello Card... 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] when else in conditional ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??
Hm...and now I’m completely stuck because apparently a conditional cannot be set at runtime in a workflow...? Ideas anyone? Thanks, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: zaterdag 30 augustus 2014 14:22 To: 'Peter Cock' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] when else in conditional ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options?? Yes, adding a when else option would be nice. However, what I really would like to have is a way to tell in one select box which other select box(es) should be refreshed when its value is changed by the user. For example: param name=cmb_col_type type=select label=Select column type param_to_refresh_on_change=cmb_polarity display=radio dynamic_options='get_column_type(library_file)' help= / param name=cmb_polarity type=select label=Select polarity display=radio dynamic_options='filter_column(library_file,cmb_col_type)' help= / So when cmb_col_type is changed, the dynamic_options of cmb_polarity are generated again by a new call to the function configured. I can create a Trello card, but I’m just wondering whether this is not already being planned by the team, especially with the Javascript/AJAX rework that is now planned/going on(?) for some time on the user interface? Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: zaterdag 30 augustus 2014 0:58 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] when else in conditional ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options?? On Fri, Aug 29, 2014 at 11:43 PM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: So I need to refresh on changeI see that if I have a conditional item in my form, this causes a refresh of the page and a (re)evaluation of my dynamic_options methodsso I could misuse this “feature”. This is deliberate, although there has been talk of updating the conditional code to do the dependent parameters dynamically rather than server-side with a page refresh. From your outline description, I think you should be using the Galaxy conditional tag. However, it seems that when I have a conditional I must have a when entry for every item in my select box. There is no “when else” option? I think you are right - I've asked in the past about this, e.g. this discussion which appears not to have been fully on the mailing list though: http://dev.list.galaxyproject.org/Multiple-values-in-lt-when-gt-tags-for-lt-conditiona-gt-parameters-tc4659704.html#none This probably deserves to be tracked with a Trello Card... 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] when else in conditional ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??
So I need to refresh on changeI see that if I have a conditional item in my form, this causes a refresh of the page and a (re)evaluation of my dynamic_options methodsso I could misuse this feature. However, it seems that when I have a conditional I must have a when entry for every item in my select box. There is no when else option? Thanks, Pieter From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: woensdag 27 augustus 2014 22:37 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] refresh_on_change : is this a valid attribute? Any other ideas/options?? Hi, I'm trying to get a wrapper from someone else working and I found this refresh_on_change attribute in his select boxes which are filled using the dynamic_options feature: param name=col_type type=select label=Select column type refresh_on_change=true display=radio dynamic_options='get_column_type(library_file)' help= / param name=polarity type=select label=Select polarity refresh_on_change=true display=radio dynamic_options='filter_column(library_file,col_type)' help= / ... When searching the documentation/wiki I do not find a reference to this, but it would be a nice option to have ;) Question: is there any way I can force a refresh when the user selects another option from such a select box. As you can see in the example above, this is needed because the next select box has its dynamic options built up by a function that takes the value from the previous select (col_type - highlighted above) as an input parameter. Currently this tool only works by showing each select in its own page , which is a deprecated option and prevents the tool from being used in a workflow... :( Thanks for your help! Best regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] refresh_on_change : is this a valid attribute? Any other ideas/options??
Hi, I'm trying to get a wrapper from someone else working and I found this refresh_on_change attribute in his select boxes which are filled using the dynamic_options feature: param name=col_type type=select label=Select column type refresh_on_change=true display=radio dynamic_options='get_column_type(library_file)' help= / param name=polarity type=select label=Select polarity refresh_on_change=true display=radio dynamic_options='filter_column(library_file,col_type)' help= / ... When searching the documentation/wiki I do not find a reference to this, but it would be a nice option to have ;) Question: is there any way I can force a refresh when the user selects another option from such a select box. As you can see in the example above, this is needed because the next select box has its dynamic options built up by a function that takes the value from the previous select (col_type - highlighted above) as an input parameter. Currently this tool only works by showing each select in its own page , which is a deprecated option and prevents the tool from being used in a workflow... :( Thanks for your help! Best regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id
Hi Dannon, I'm facing the same problem now. Could you help me with the steps to delete the migrate_tmp table manually? I'm trying to use sqlite from command line but get the following error: Unable to open database universe.sqlite: file is encrypted or is not a database Thanks and regards, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Dannon Baker Sent: dinsdag 18 februari 2014 14:40 To: Peter Cock Cc: Galaxy Dev Subject: Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com wrote: This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Yes, I've seen this before when I've killed (or otherwise crashed) a migration in process; migrate_tmp doesn't get automatically cleaned up -- and, to allow for recovery, probably shouldn't.Any idea what may have caused it in your case?For a development database I've most commonly just deleted the migrate_tmp table manually and rerun the migration. It's worth noting that *only* sqlite can have this problem, due to the way migrations work. -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/
Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id
Hi Dannon, Thanks, this helped. Just for the record: I did find a small typo in my mail and in your script : should be migration_tmp instead of migrate_tmp;) Best regards, Pieter. From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: dinsdag 22 april 2014 14:59 To: Lukasse, Pieter Cc: Peter Cock; Galaxy Dev Subject: Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id Hey Pieter, sure. The sqlite database is in sqlite3 format, so you'll need to use 'sqlite3 database/universe.sqlite' to access it. The following should work: sqlite3 database/universe.sqlite '.dump migrate_tmp' temporary_backup.sql sqlite3 database/universe.sqlite 'drop table migrate_tmp;' And, once that's done, verify that everything works as expected and that whatever table is in temporary_backup.sql actually did get migrated. -Dannon On Tue, Apr 22, 2014 at 8:41 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi Dannon, I’m facing the same problem now. Could you help me with the steps to delete the migrate_tmp table manually? I’m trying to use sqlite from command line but get the following error: Unable to open database universe.sqlite: file is encrypted or is not a database Thanks and regards, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Dannon Baker Sent: dinsdag 18 februari 2014 14:40 To: Peter Cock Cc: Galaxy Dev Subject: Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com wrote: This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Yes, I've seen this before when I've killed (or otherwise crashed) a migration in process; migrate_tmp doesn't get automatically cleaned up -- and, to allow for recovery, probably shouldn't.Any idea what may have caused it in your case?For a development database I've most commonly just deleted the migrate_tmp table manually and rerun the migration. It's worth noting that *only* sqlite can have this problem, due to the way migrations work. -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/
Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week
Hi Alex, all
FYI - I've added the card to https://trello.com/c/ro8knsaa some time ago. Can
you please vote for it?
Thanks,
Pieter.
From: Bossers, Alex
Sent: dinsdag 25 maart 2014 16:52
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Strange issue with datatypes in Galaxy version of
last week
Pieter,
I just experienced the same with another generic tabular .tab file output. It
broke the filename at dash without any extension.
The file itself was ok, just the name.
Alex
Van:
galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Lukasse, Pieter
Verzonden: dinsdag 25 maart 2014 16:33
Aan: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] Strange issue with datatypes in Galaxy version of last
week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
datatype extension=msclust.csv type=galaxy.datatypes.tabular:Tabular
mimetype=text/csv display_in_upload=true subclass=true/
At first Galaxy output seems fine:
[cid:image001.png@01CF4FF4.E1830B70]
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to edit attributes and just click save, then upon downloading
again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
inline: image001.png___
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[galaxy-dev] Strange issue with datatypes in Galaxy version of last week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
datatype extension=msclust.csv type=galaxy.datatypes.tabular:Tabular
mimetype=text/csv display_in_upload=true subclass=true/
At first Galaxy output seems fine:
[cid:image001.png@01CF4847.DE4A1A70]
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to edit attributes and just click save, then upon downloading
again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
inline: image001.png___
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Re: [galaxy-dev] Question on storage configuration for Galaxy datasets
Hi all, Could someone comment on my question below ? I see that a similar question from Eric (with title object_store_conf.xml route users to different storage ) is also unanswered. Thanks for your help, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 30 januari 2014 11:10 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Question on storage configuration for Galaxy datasets Hi , We would the location of the datasets our Galaxy stores to be determined dynamically based on a set of rules. For example: for a specific role we would like a datasets to be stored in a folder /storage/no_backup and for another role this should be /storage/with_backup Is there currently a configuration file in Galaxy to set this up? Or perhaps any alternative solutions? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Question on storage configuration for Galaxy datasets
Hi , We would the location of the datasets our Galaxy stores to be determined dynamically based on a set of rules. For example: for a specific role we would like a datasets to be stored in a folder /storage/no_backup and for another role this should be /storage/with_backup Is there currently a configuration file in Galaxy to set this up? Or perhaps any alternative solutions? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Toolbox filtering question
Hi, I would like specify a filter based on a role. Does someone know how to do this? I already have an example on how to do this based on user id (found at https://wiki.galaxyproject.org/UserDefinedToolboxFilters#For_Administrators) but now I would like to filter out menu items in case users don't have a specific role. Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolbox filtering question
Ok, just answering my own question ;) I found a solution, here it goes (also attached): import logging log = logging.getLogger( __name__ ) def restrict_prims_metabolomics( context, tool ): This tool filter will hide MsClust for non-metabolomics users. This can be enabled by adding the following to the ``app:main`` section of ``universe_wsgi.ini``:: tool_filters = primsfilters:restrict_prims_metabolomics # for debugging: import pydevd;pydevd.settrace(L0136815.wurnet.nl) user = context.trans.user metabolomics_tools = [ MsClust, textutil, filter ] if tool.name in metabolomics_tools: # logging.warn( 'FILTER MATCHED: %s' %(tool.name)) for user_role in user.roles: if user_role.role.name == PRIMS_METABOLOMICS: return True # not found to have the role, return false: return False else: # return true for any other tool return True From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 30 januari 2014 14:25 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Toolbox filtering question Hi, I would like specify a filter based on a role. Does someone know how to do this? I already have an example on how to do this based on user id (found at https://wiki.galaxyproject.org/UserDefinedToolboxFilters#For_Administrators) but now I would like to filter out menu items in case users don't have a specific role. Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ primsfilters.py Description: primsfilters.py ___ 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] repository metadata reset not always working
Hi Greg, Thanks for this. I have been observing the behaviour more closely and actually it looks like there could be a related issue: sometimes after resetting the metadata if reported as successfully finished it still takes some time (~3 minutes?) before all changes are also really visible in the UI (e.g. when clicking on one of the repositories again in the list repositories I own). Regards, Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: maandag 30 december 2013 16:39 To: Lukasse, Pieter Cc: galaxy-...@bx.psu.edu Subject: Re: repository metadata reset not always working Hello Pieter, I've added the following Trello card for this issue - we'll take a looke as soon as possible. https://trello.com/c/LZ3Lj9ye/125-problem-with-adding-deleting-adding-readme-files Thanks for reporing this, Greg Von Kuster On Dec 30, 2013, at 8:09 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi Greg, I found an issue in Toolshed, not sure if it has been reported before. Steps: 1-Make a repository and add a tool .xml and a README file 2-Reset metadata and check if all information appears in the toolshed UI 3-Now delete the README file from the hg repository 4-Commit 5-(not sure whether I did this step) reset metadata 6-Now add the README file back but with different contents. Commit, reset metadata 7-In the toolshed UI you will see that the OLD REAME contents are displayed. This is just one example...I have the feeling it is not restricted to the README files of course...so it can be quite a serious issue. Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] repository metadata reset not always working
Hi Greg, I found an issue in Toolshed, not sure if it has been reported before. Steps: 1-Make a repository and add a tool .xml and a README file 2-Reset metadata and check if all information appears in the toolshed UI 3-Now delete the README file from the hg repository 4-Commit 5-(not sure whether I did this step) reset metadata 6-Now add the README file back but with different contents. Commit, reset metadata 7-In the toolshed UI you will see that the OLD REAME contents are displayed. This is just one example...I have the feeling it is not restricted to the README files of course...so it can be quite a serious issue. Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked
Hi Peter,
Galaxy starts, but any operation that involves changes in the database seems to
fail.
One solution I found was to move to the default branch (hg update default)
instead of the stable one...there the problem seems to be fixed somehow.
However, then I get another error when trying to create a new history because
the attribute genome_build in the payload is null and, according to the
error, it should be a string. Details:
source
annotation
deleted
false
genome_build
null
id
cc4287507a7e4aae
model_class
History
name
test1235
nice_size
0 bytes
published
false
purged
false
state
new
state_details
discarded
0
empty
0
error
0
failed_metadata
0
new
0
ok
0
paused
0
queued
0
running
0
setting_metadata
0
upload
0
state_ids
discarded
empty
error
failed_metadata
new
ok
paused
queued
running
setting_metadata
upload
tags
url
/api/histories/cc4287507a7e4aae
user
username
pieterlukasse
quota_percent
null
total_disk_usage
36654268543
nice_total_disk_usage
34.1 GB
email
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl
model_class
User
id
f2db41e1fa331b3e
diskSize
0
xhr
readyState
4
responseText
{ error: genome_build must be a string: }
responseJSON
error
genome_build must be a string:
status
400
statusText
Bad Request
responseHeaders
Date
Wed, 18 Dec 2013 13:43:26 GMT
cache-control
max-age=0,no-cache,no-store
Server
PasteWSGIServer/0.5 Python/2.7.5+
Connection
close
content-type
application/json
options
validate
true
parse
true
emulateHTTP
false
emulateJSON
false
Disabling this specific validation in
/home/lukas007/galaxy-dist/lib/galaxy/webapps/galaxy/api/histories.py (by
disabling I mean just putting a dummy string value in genome_build) will
restore the normal Galaxy functionality and all seems to be working fine
now...until I hit something that depends on this genome_build parameter of
course... Is this a known issue? If not, hereby ;)
Regards,
Pieter.
-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: woensdag 18 december 2013 17:36
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: New Galaxy won't start, SQLite (OperationalError) database is
locked
On Wed, Dec 18, 2013 at 12:51 PM, Lukasse, Pieter
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote:
Hi Peter,
I know that ;) Still I am curious about the possible solution. Any ideas?
Regards,
Pieter.
Could you clarify the nature of the problem - is it failing to even start as in
the situation I reported at the start of this thread, or an intermittent
problem?
Note that while generally stable I have had problems with my development
machine with heavy SQLite DB access, e.g. a large multi-part job being split
creating many child jobs in quick succession.
Peter
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Re: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked
Hi Peter, Thanks for reporting this. I am now facing the same error, but I don't get it For example: normally it appears when I try to change something in the DB (e.g. adding a new history), but then suddenly I managed to create one new history itemand now it is occurring again. It seems to be a transient locked state, so every now and then the lock is released somehow. Anyway, are there any ideas on what could be a real solution to this problem? This is the second Galaxy server I upgrade which now is stuck after the upgrade...any help is appreciated! Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock Sent: donderdag 31 oktober 2013 11:54 To: Galaxy Dev Subject: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked Hello all, While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite), $ hg clone https://bitbucket.org/galaxy/galaxy-dist ... $ cd galaxy-dist $ ./run.sh ... galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked u'PRAGMA table_info(dataset)' () After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think). Repeating the experiment under /tmp on a local hard disk worked :) (I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error) 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/ 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] New Galaxy won't start, SQLite (OperationalError) database is locked
Hi Peter, I know that ;) Still I am curious about the possible solution. Any ideas? Regards, Pieter. From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: woensdag 18 december 2013 13:31 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: New Galaxy won't start, SQLite (OperationalError) database is locked Hi Pieter, Using SQLite is NOT recommended for a production Galaxy, it is only really used for development and testing (having the whole database as one file on disk without worrying about creating a proper database, user accounts etc is nice). Peter On Wednesday, December 18, 2013, Lukasse, Pieter wrote: Hi Peter, Thanks for reporting this. I am now facing the same error, but I don't get it For example: normally it appears when I try to change something in the DB (e.g. adding a new history), but then suddenly I managed to create one new history itemand now it is occurring again. It seems to be a transient locked state, so every now and then the lock is released somehow. Anyway, are there any ideas on what could be a real solution to this problem? This is the second Galaxy server I upgrade which now is stuck after the upgrade...any help is appreciated! Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edujavascript:; [mailto:galaxy-dev-boun...@lists.bx.psu.edujavascript:;] On Behalf Of Peter Cock Sent: donderdag 31 oktober 2013 11:54 To: Galaxy Dev Subject: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked Hello all, While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite), $ hg clone https://bitbucket.org/galaxy/galaxy-dist ... $ cd galaxy-dist $ ./run.sh ... galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked u'PRAGMA table_info(dataset)' () After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think). Repeating the experiment under /tmp on a local hard disk worked :) (I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error) 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/ 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] problems with exporting or importing data from file
Hi Jeremy, Anna, I'm having a similar problem here as well. I would like to get a history from one Galaxy server to another and I followed the export and import steps. I even did a wget at the destination Galaxy server to check whether it could download the tar.gz file and this worked. When using the web UI I also get this message on my log showing it is actually doing something when I trigger the import: 10.85.13.89 - - [18/Dec/2013:15:10:48 +0200] POST /history/import_archive HTTP/1.1 200 - http://dev1.ab.wurnet.nl:8088/history/import_archive; Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36 galaxy.jobs DEBUG 2013-12-18 15:10:48,391 (3201) Working directory for job is: /home/lukas007/galaxy-dist/database/job_working_directory/003/3201 galaxy.jobs.handler DEBUG 2013-12-18 15:10:48,404 (3201) Dispatching to local runner galaxy.jobs DEBUG 2013-12-18 15:10:48,478 (3201) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-12-18 15:10:48,514 (3201) Job dispatched galaxy.jobs.runners.local DEBUG 2013-12-18 15:10:48,742 (3201) executing: export GALAXY_SLOTS=1; python /home/lukas007/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://galaxy.wur.nl/galaxy_production/history/export_archive?id=b1f249e032330dc4 /home/lukas007/galaxy-dist/database/tmp/tmpPGL6le --url galaxy.jobs DEBUG 2013-12-18 15:10:48,786 (3201) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-12-18 15:10:48,875 execution finished: export GALAXY_SLOTS=1; python /home/lukas007/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://galaxy.wur.nl/galaxy_production/history/export_archive?id=b1f249e032330dc4 /home/lukas007/galaxy-dist/database/tmp/tmpPGL6le --url galaxy.jobs DEBUG 2013-12-18 15:10:49,040 job 3201 ended galaxy.datatypes.metadata DEBUG 2013-12-18 15:10:49,040 Cleaning up external metadata files However, nothing is visible in my histories list. What could be wrong? I also don't see any error messages in the log above. Thanks and regards, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Jeremy Goecks Sent: dinsdag 11 juni 2013 19:06 To: Edlund, Anna Cc: galaxy-...@bx.psu.edu; Nicola Segata Subject: Re: [galaxy-dev] problems with exporting or importing data Anna, Try following these steps: (1) Make your history accessible (Share or Publish -- Make History Accessible by Link). (2) Export your history again; make sure to wait until you can use the URL to download a .gz file of your history. (3) Try importing it via URL to the Huttenhower Lab Galaxy. Let us know if you have any problems. Best, J. On Jun 10, 2013, at 11:45 AM, Edlund, Anna wrote: Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select 'Import a History from an archive'. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedl...@jcvi.orgmailto:aedl...@jcvi.org ___ 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] Supporting file sets for running a tool with multiple input files
Hi Dannon, Thanks for your reply. I've found a workaround by using the method Binary.register_sniffable_binary_format() . I discovered this workaround in a previous thread by John Chilton. Attached the complete solution, just for the record. Regards, Pieter. From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: maandag 4 november 2013 13:42 To: Lukasse, Pieter Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Supporting file sets for running a tool with multiple input files Hi Pieter, We've worked out what we think is the right way to solve this for Galaxy and expect work to start soon. See the trello card (https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more details. For your particular tool, the first workaround that comes to mind would be adding a new datatype, say, ZippedInputFiles in your toolshed repository that gets included and used by users, though I haven't actually tried that. That said, I'd probably wait, this feature is high on our list of things to do next. -Dannon On Mon, Nov 4, 2013 at 5:44 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891tel:%2B31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ prims_masscomb_datatypes.py Description: prims_masscomb_datatypes.py ?xml version=1.0? datatypes datatype_files datatype_file name=prims_masscomb_datatypes.py/ /datatype_files registration display_path=display_applications datatype extension=prims.fileset.zip type=galaxy.datatypes.prims_masscomb_datatypes:FileSet display_in_upload=true/ /registration /datatypes___ 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] Supporting file sets for running a tool with multiple input files
Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Hi Greg, The strange thing is that the tool loads fine in my local Galaxy server (so not using toolshed but the old-fashioned way). The difference could be that my Galaxy server is not up to date and perhaps using a different xml parsing scheme? Anyway, are there XSD files which I could use to run some more detailed validations? Thanks, Pieter. -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: dinsdag 29 oktober 2013 13:29 To: Lukasse, Pieter Cc: galaxy-...@bx.psu.edu Dev Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hi Pieter, The tool shed is undoubtedly not the problem here. The tool is simply not identified as a Galaxy tool for some reason. When it had xml validation errors, it was not loaded as a Galaxy tool due to the errors. I'm not sure what new issue is causing the xml to not load properly as a Galaxy tool. But Peter's direction is correct - discover why the xml file is not properly loading into Galaxy as a Galaxy tool. The Tool Shed uses virtually the same loading process as Galaxy. I'm travelling currently, but I'll try to get some time ove rhte next couple of days to look at this again if you haven't been able to discover the cause of the problem. Thanks, Greg Von Kuster On Oct 29, 2013, at 7:00 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Oct 29, 2013 at 6:23 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, what I mean is that I don't expect any other errors in my files since I corrected the errors you reported. When using my XML editor I also don't get any errors, so the files seem OK. However, the problem remains: one of the tools and also the dependencies definitions don't appear in the toolshed package. Are there .xsd files I can check these files against? As far as I know there are no XML schema definitions for the Galaxy tool definition format (e.g. DTD files), so this cannot be fully validated by an XML validator. As your problem, according to the Tool Shed you have four valid tools: http://testtoolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb * MsPicture * FASTA validator * DB Search Converter * Mascot The missing (invalid) tool is masscomb_dbsearch_xtandem.xml - X Tandem. Does the tool work on your local Galaxy instance? If so then it seems the Tool Shed is being too strict, or failing to parse this tool for some reason. 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/ 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] Tool refuses to appear in Toolshed package contents
Hi Bjoern, Indeed resetting the metadata solved the problem. Thanks! Best regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: woensdag 30 oktober 2013 15:16 To: Lukasse, Pieter Cc: Greg Von Kuster (g...@bx.psu.edu); galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hi Pieter, I tried to reproduce it and looked over your files. I also tried to reproduce it and can't. For me its showing up nicely: http://testtoolshed.g2.bx.psu.edu/view/bgruening/upload_testing So please try to reset metadata of that repository. And hopefully your issues are gone magically :) Cheers, Bjoern Hi , I have a toolshed repository where I expect 5 tools to appear in the “Contents of this repository” section but one of them fails to appear in the list (see screenshot). Where can I find out what is going wrong? Thanks, Pieter. Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.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/ 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] Tool refuses to appear in Toolshed package contents
Hi Greg, what I mean is that I don't expect any other errors in my files since I corrected the errors you reported. When using my XML editor I also don't get any errors, so the files seem OK. However, the problem remains: one of the tools and also the dependencies definitions don't appear in the toolshed package. Are there .xsd files I can check these files against? Thanks and regards, Pieter. From: Greg Von Kuster [g...@bx.psu.edu] Sent: Friday, October 25, 2013 3:57 PM To: Lukasse, Pieter Cc: 'Peter Cock'; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hi Pieter, Perhaps I'm misunderstanding this issue. Can you clarify the problem? Thanks, Greg Von kuster On Oct 25, 2013, at 9:53 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Kind of assuming Greg did this yesterday when he replied with only two problemsbut you are right, I can check the XML correctness locally (although this does not solve the fundamental problem). Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: vrijdag 25 oktober 2013 15:49 To: Lukasse, Pieter Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Regards, Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: donderdag 24 oktober 2013 17:29 To: Lukasse, Pieter Cc: 'Peter Cock'; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hello Pieter, There are 2 different issues in 2 of your xml files that make them invalid XML. 1. In your tool_dependencies.xml file, you need to close the version string attribute in the package tag. So the following line with the problem: package name=xtandem version=12.10011 is fixed when it looks like this: package name=xtandem version=12.10011 2. In your mass comb_dbsearch_xtandem.xml file, the comment outside of the /tool tag on the last line problematic. /tool !-- NB: edit /etc/profile and add the xtandem bin folder to PATH -- The above XML results in the XML document being parsed such that the XML root is the comment itself. If you move the comment line insideo of the tool tag set, all is well: !-- NB: edit /etc/profile and add the xtandem bin folder to PATH -- /tool Unfortunartely, it is difficult to render meaningful messages for invalid XML like this as the XMNL parser does not provide much of anything meaningful that can be passed on in the UI. At some point I may find the chance to incorporate a validator, but just don't currently have the time. Greg Von Kuster On Oct 24, 2013, at 10:46 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi Peter, I've added the package to the test toolshed now as well, but there the revision is not seen in the metadata (see screenshot). What is needed to get this repository active? Is this still the reset metadata (is this a bug or by design)? Thanks for your help! image001.jpg Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.comhttp://googlemail.com] Sent: donderdag 24 oktober 2013 13:27 To: Lukasse, Pieter Cc: Greg Von Kuster (g...@bx.psu.edumailto:g...@bx.psu.edu); galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Thu, Oct 24, 2013 at 12:09 PM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi , I have a toolshed repository where I expect 5 tools to appear in the Contents of this repository section but one of them fails to appear in the list (see screenshot). Where can I find out what is going wrong? Thanks, Pieter. Hi Pieter, The first thing to confirm is if the missing tool a valid XML file? Next, does it work in your Galaxy instance (if installed manually). Now if this problem is only in the Tool Shed, which toolshed is it in? Your own local tool shed, the main Penn State public Tool Shed, the Penn State Test Tool Shed, or somewhere else? If it is your own tool shed, you should be able to look at its logging for clues. If it is a public tool shed, please share the URL for the repository. 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/ 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] Tool refuses to appear in Toolshed package contents
Kind of assuming Greg did this yesterday when he replied with only two problemsbut you are right, I can check the XML correctness locally (although this does not solve the fundamental problem). Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: vrijdag 25 oktober 2013 15:49 To: Lukasse, Pieter Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problems with toolshed package update process
Hi Greg, Yes, we have an older Mercurial installation (2.0.2 !) . We will try a newer version. Thanks! Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: vrijdag 13 september 2013 13:56 To: Lukasse, Pieter Cc: Kuijt, Eric; 'galaxy-...@bx.psu.edu' Subject: Re: problems with toolshed package update process Hello Pieter, The version of mercurial you are using is likely older than version 2.2.3. See: http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line Can you check this? Greg Von Kuster On Sep 13, 2013, at 5:54 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi Greg, We have been trying out the update process as follows: 1-Make changes to one of the files in the repository 2-Commit and push changes to hg After these two steps we expected to be able to update the tool in Galaxy. However this was not possible. We noticed that every time we pushed a new revision to the toolshed hg we had to use the option Reset all repository metadata, i.e. the new revision would be seen as an update only after doing this reset. Is this the normal behaviour? I can imagine that in some cases the admin would like to review a new committed changeset before enabling it as an update...could it be this is a configuration we forgot to change somewhere? Best regards, Pieter. image001.png Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] toolshed tool versions and tool panel
Hi Greg, When updating the version number of a tool I noticed that, as expected, both the old version and the new version of the tool become available in the Galaxy environment. What I did not expect is that the new version resulted in a new entry in the menu bar (see screenshot): [cid:image001.png@01CEB07A.3ECB90B0] If I remember correctly, you showed in Oslo that the tool version becomes a choice in the tool itself, something like the screenshot below: [cid:image002.png@01CEB07A.9929B870] Is this a setting somewhere or are we facing a bug? Best regards, Pieter. Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ inline: image001.pnginline: image002.png___ 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] HOWTO for making new toolshed package
Ok, cool...I get the picture. One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicableI'm just thinking of scenarios where there is a bad update released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern Hi Greg, Fantastic, thanks for your detailed answer! I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ? Regards, Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new toolshed package Hello Pieter, Please send questions like this to the galaxy-...@bx.psu.edu or galaxy-dev@lists.bx.psu.edu mailing list rather than individual email addresses to ensure optimal, timely responses. The Tool Shed wiki contains all of the information you need: http://wiki.galaxyproject.org/Tool%20Shed This page provides a nice overview of repository features: http://wiki.galaxyproject.org/ToolShedRepositoryFeatures See additional specific pages below for each item you've listed: On Sep 11, 2013, at 11:52 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, I want to make a toolshed package with the following contents: The above package is actually a mercurial repository in the tool shed. · A number of tools The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed. http://wiki.galaxyproject.org/ToolShedToolFeatures · Some workflows The following pages provide information for enabling workflow sharing via the Tool Shed. http://wiki.galaxyproject.org/ToolShedWorkflowSharing · Datatypes Datatype features in the Tool Shed are described in the following pages: http://wiki.galaxyproject.org/ToolShedDatatypesFeatures · Installation configurations for installing external tools like R, Gnuplot and X!Tandem The above information is document in the ToolShedToolFeatures section of the wiki, specifically in the following pages: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-par ty_tool_dependency_installation_and_compilation_with_installed_reposit ories · Dependencies configurations to other packages If by packages, you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages: http://wiki.galaxyproject.org/DefiningRepositoryDependencies Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use? Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using
Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package
Hi Bjoern, Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_location_of_images_in_tool_configuration_files We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png so the variable is not being replaced by the value of the path...is this a known issue? Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 14:31 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-ability-to-change-the-tool/diff Cheers, Bjoern One extra detail I'm trying to find in the docs but haven't found yet: How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed? Example: -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a Tool test results container when viewing or managing the repository. Greg Von Kuster On Sep 12, 2013, at 7:23 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Ok, cool...I get the picture. One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicableI'm just thinking of scenarios where there is a bad update released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern Hi Greg, Fantastic, thanks for your detailed answer! I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ? Regards, Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new
Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package
Hi guys, We discovered that the problem is at our apache configuration side...working on it now... ;) Regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 12 september 2013 16:13 To: 'Bjoern Gruening' Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Bjoern, Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_location_of_images_in_tool_configuration_files We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png so the variable is not being replaced by the value of the path...is this a known issue? Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 14:31 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-ability-to-change-the-tool/diff Cheers, Bjoern One extra detail I'm trying to find in the docs but haven't found yet: How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed? Example: -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a Tool test results container when viewing or managing the repository. Greg Von Kuster On Sep 12, 2013, at 7:23 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Ok, cool...I get the picture. One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicableI'm just thinking of scenarios where there is a bad update released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug Regards, Pieter. -Original Message- From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern Hi Greg, Fantastic, thanks for your detailed answer! I am trying out some things and I noticed
Re: [galaxy-dev] Display of HTML type broken in new Galaxy ?
Hi Joachim, By the way: do you know what the reason is for this setting? Is there a known security problem that triggered this feature? If you add only trusted tools to your Galaxy environment, then this is not needed, right? This change was mentioned briefly in March 12, 2012 Galaxy Development News Brief but no background information was given Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 18 oktober 2012 9:19 To: 'joachim.ja...@vib.be' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ? Thanks Joachim, that solved the problem! -Original Message- From: Joachim Jacob [mailto:joachim.ja...@vib.be] Sent: woensdag 17 oktober 2012 10:47 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ? Hi, Make sure that in your universe.wsgi is set: sanitize_all_html = False Hope this helps, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 10/17/2012 10:09 AM, Lukasse, Pieter wrote: Hi, I noticed that in the new Galaxy version the preview of HTML files seems to be broken. When I try to preview a HTML file generated by a tool, it displays a HTML that has all style stripped off. So the HTML display is in fact changing the generated HTML before displaying it. Has anyone noticed this as well? What are the fixes/workarounds? Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl http://www.pri.wur.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/ ___ 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] Display of HTML type broken in new Galaxy ?
Can anyone give some more information about this? Thanks, Pieter. -Original Message- From: Joachim Jacob [mailto:joachim.ja...@vib.be] Sent: donderdag 15 november 2012 9:17 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ? I have no clue at all, sorry. Cheers, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 11/15/2012 09:14 AM, Lukasse, Pieter wrote: Hi Joachim, By the way: do you know what the reason is for this setting? Is there a known security problem that triggered this feature? If you add only trusted tools to your Galaxy environment, then this is not needed, right? This change was mentioned briefly in March 12, 2012 Galaxy Development News Brief but no background information was given Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 18 oktober 2012 9:19 To: 'joachim.ja...@vib.be' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ? Thanks Joachim, that solved the problem! -Original Message- From: Joachim Jacob [mailto:joachim.ja...@vib.be] Sent: woensdag 17 oktober 2012 10:47 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ? Hi, Make sure that in your universe.wsgi is set: sanitize_all_html = False Hope this helps, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 10/17/2012 10:09 AM, Lukasse, Pieter wrote: Hi, I noticed that in the new Galaxy version the preview of HTML files seems to be broken. When I try to preview a HTML file generated by a tool, it displays a HTML that has all style stripped off. So the HTML display is in fact changing the generated HTML before displaying it. Has anyone noticed this as well? What are the fixes/workarounds? Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl http://www.pri.wur.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/ ___ 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] Validation / validator questions
Hi, Is it possible to do validation of input fields depending on the value of OTHER input fields? Example 1 If field A is filled, then field B also should be filled. Example 2 Field B should be field A etc Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/
Re: [galaxy-dev] Display of HTML type broken in new Galaxy ?
Thanks Joachim, that solved the problem! -Original Message- From: Joachim Jacob [mailto:joachim.ja...@vib.be] Sent: woensdag 17 oktober 2012 10:47 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ? Hi, Make sure that in your universe.wsgi is set: sanitize_all_html = False Hope this helps, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 10/17/2012 10:09 AM, Lukasse, Pieter wrote: Hi, I noticed that in the new Galaxy version the preview of HTML files seems to be broken. When I try to preview a HTML file generated by a tool, it displays a HTML that has all style stripped off. So the HTML display is in fact changing the generated HTML before displaying it. Has anyone noticed this as well? What are the fixes/workarounds? Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl http://www.pri.wur.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/ ___ 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] Display of HTML type broken in new Galaxy ?
Hi, I noticed that in the new Galaxy version the preview of HTML files seems to be broken. When I try to preview a HTML file generated by a tool, it displays a HTML that has all style stripped off. So the HTML display is in fact changing the generated HTML before displaying it. Has anyone noticed this as well? What are the fixes/workarounds? [cid:image001.jpg@01CDAC4F.72D92640] Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ inline: image001.jpg___ 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] Avoiding same dataset selection
Hi, Is there a way to use validator or perhaps filter options to avoid the selection of the same dataset twice in different parameters of a tool. E.g. a tool has 2 data type parameters of the same type, but it should not be possible for the user to set both parameters to the same dataset. So if his history contains files A,B, and C and he selects A in his first parameter, then the second parameter should display only the options B and C. Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.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/
[galaxy-dev] Mapping input fields in a workflow
Hi, Is there any way to map an input field from one tool to the input field of another tool in a workflow? E.g. let's say tool A has an input field X which tool B also has. If we use both tool A and B in the same workflow, then we would like to let the user fill in field X only once in tool A and then map that value to the field X in tool B. As far as I can see, there is now only a way to map output files of tool A to input files of tool B. [cid:image001.png@01CDA2E2.20BC4390] Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ inline: image001.png___ 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] Local display application questions
Hi Greg,
I made a tool for Galaxy which produces a normal XML output file and next to
that it also produces a HTML report with some quick summarized details for the
user.
I could solve this by using 2 output files, but I don't want to keep the
history as concise as possible. To I found the option to use display
application. I defined my as below:
display id=sedmatreport version=1.0.0 name=Show
link id=sedmatreport name=SedMat_report
url
target_frame=galaxy_main${BASE_URL}/static/prims/reports/${dataset.id}/sedmat_report.html/url
/link
/display
So in my tool config xml I have the following respective configuration:
command interpreter= java -jar
Mytool.jar
...some parameters
-outReport
/galaxy-dist/static/prims/reports/$outputData.dataset.id/sedmat_report.html
#end if
/command
è This works fine, but I would like to avoid using the static directory. Do
you know if there is an alternative web directory configured by default in the
Galaxy web-server?
è
è I also want to avoid the /galaxy-dist/ part in the tool configuration since
the Galaxy home directory can vary. Is there a variable which I can use for
this?
Thanks and regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
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[galaxy-dev] External/custom display applications
Hi,
Is there more documentation on the topic of custom display applications?
I only found
http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial
which has a few examples, but these are incomplete. For example, they use some
variables like ${BASE_URL} and ${DATASET_HASH} but I cannot find extra
information on these and if there are more variables which I could use.
Basically I want to build a tool which also its own display application next to
the normal textual output file.
Thanks and regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
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[galaxy-dev] Questions about reusing workflows
Hi, I have some questions about adding new custom tools to my Galaxy instance: 1-How can I reuse workflows? a.Should I wrap a workflow as a tool? b.Or can I just add a custom workflow as a workflow step in another workflow? 2-I noticed that option 1.b above seems to copy the complete workflow into my new workflow, so if I have an existing workflow A with N steps and want to use this in workflow B which already has M steps, I end up with a workflow that has M+N steps while I would expect M+1 steps... This behaviour gives me the impression that if I change workflow A, this will not automatically imply a change in workflow B. Is my interpretation correct? 3-If option 1.a above is the way to go for now, what are the steps to do this? E.g. what is the command to run a workflow from the command line? Thanks and regards, Pieter Lukasse. ___ 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] Questions about reusing workflows
Hi Peter, Thanks for the reply. Does anyone know how to execute a specific workflow from the command prompt? E.g. run the workflow as a job? Then I could perhaps write a workflow wrapper tool to overcome this shortcoming. Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: donderdag 13 oktober 2011 12:34 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Questions about reusing workflows Hi Pieter, You cannot currently embed on workflow within another, although that has been suggested as a nice extension to Galaxy. You can for instance start a new history, run workflow #1 with N tool steps, then workflow #2 with M tool steps, and save this history as a new workflow #3 with N+M tool steps. This has the downside that if either workflow #1 or #2 is changed, this does not alter #3 - which is an independent copy. 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/
