[galaxy-dev] Running additional services

[Rob Leclerc]

We're running cloudman and I would like to run a couple of additional
services alongside galaxy. Is there a elegant way/place to add/run these
services to existing galaxy code/scripts?

Cheers,
Rob


Rob Leclerc, PhD
 
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
Personal Email: rob.lecl...@aya.yale.edu
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Re: [galaxy-dev] CloudMan Error

[Dannon Baker]

The warning message printed by the first ssh attempt indicates that you
have no cloudman_key_pair.pem in the directory you executed the ssh command
from.  Find this file (or create a new one) and you'll be able to ssh.

Good luck, and please keep threads on the list instead of emailing
directly.  Thanks!

-Dannon

On Mon, Jul 22, 2013 at 1:36 PM,  wrote:

> Hi- the share string appears to be loading, but I am unable to ssh into my
> instance using the provided command, or anything like it. Instead I get the
> following:
>
> denizerezyilmaz$ ssh -i cloudman_key_pair.pem
> ubu...@ec2-54-242-61-164.compute-1.amazonaws.com
> Warning: Identity file cloudman_key_pair.pem not accessible: No such file
> or directory.
>
> OR:
>
>  denizerezyilmaz$ ssh ec2-54-242-61-164.compute-1.amazonaws.com
> Permission denied (publickey).
>
> What am I missing? Thank you, Deniz
>
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Re: [galaxy-dev] Cloudman - is it possible to still use depreciated AMIs ?

[Dannon Baker]

Yes, you can still use the deprecated AMIs.  What error are you seeing when
you try to ssh in?


On Mon, Jul 22, 2013 at 4:30 PM, Ravpreet Setia
wrote:

>  I tried launching an instance specifying "ami-da58aab3" as the AMI but I
> am unable to SSH or access Cloudman using the instance's URL.
>
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Re: [galaxy-dev] Cloudman master cannot connect to volume at start-up

[Dannon Baker]

Can you verify that the volume does still exist in your account, and that
you're launching from the same availability zone that the volume exists in?


On Mon, Jul 22, 2013 at 4:13 PM, Ravpreet Setia
wrote:

>
>- This is what has been reported by the cluster status log:
>-
>- 20:01:14 - Master starting
>- 20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb:
>EC2ResponseError: 400 Bad Request**InvalidVolume.NotFound**The
>volume 'vol-91cfd1cb' does not exist.
>9179663c-c5ec-4e90-88ff-ecf606b5e9a6
>- 20:01:16 - Attempting to connect to a non-existent volume
>vol-91cfd1cb
>- 20:01:16 - Error processing filesystems in existing cluster
>configuration: 'NoneType' object has no attribute '__getitem__'
>- 20:01:16 - * Manager failed to start *
>
>
>  Any suggestions?
>
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Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome

[Moritz Juchler]

Hey,

now I am having a new problem: *Convert SAM to BAM
*Tool execution generated the following error message:

[samopen] SAM header is present: 93 sequences.
Parse error at line 106: sequence and quality are inconsistent
/bin/sh: line 1: 27934 Aborted samtools view -bS
"/home/trr/galaxy-dist/database/files/000/dataset_17.dat" >
"/tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam"

The tool produced the following additional output:

[bam_header_read] EOF marker is absent. The input is probably truncated.

(should I make a new post out of this?)

The step I did before was:
7: *Map* with BWA for Illumina on data 5 and data 3: mapped reads
~21,000 lines, 94 comments
format: sam, database: hg19
 BWA Version: 0.7.5a-r405 BWA run on paired-end data

That one seems to work correctly.
Any help appreciated :)

Best
Moritz


On 22 July 2013 11:20, Moritz Juchler wrote:

> Hey,
>
> with the "tool file" line I got it working :)
> Thanks a lot. Could you answer the question regarding Tool Shed: "If I
> would use Tool Shed, could I skip all these manual steps? Is the
> installation of BWA with Tool Shed also this complicated or is it more
> simle?"
>
> Best
> Moritz
>
>
> On 17 July 2013 09:51, Moritz Juchler wrote:
>
>> Hey,
>>
>> no thats correct I did not use Tool Shed. If I would use it, could I skip
>> all these manual steps? Is the installation of BWA with Tool Shed also this
>> complicated or is it more simle?
>>
>> How did you not follow my steps :) I wrote down everything clearly, at
>> least thats what I was hoping.
>>
>> And no I didnt write this line " > />" Thats the first time, I am seeing this tutorial :( I will try this
>> out right now
>>
>> Best
>> Moritz
>>
>>
>> On 17 July 2013 09:42, Hans-Rudolf Hotz  wrote:
>>
>>> Hi Moritz
>>>
>>> I am struggling to follow what exactly you have done. As far as I can
>>> see, you did not use the toolshed (http://wiki.galaxyproject.**
>>> org/Tool%20Shed ) to install
>>> the BWA alinger tool, but did all manually?
>>>
>>> If so, have you added the following line:
>>>
>>>  
>>>
>>> to the "tool_conf.xml" file, and restarted Galaxy?
>>>
>>>
>>> see also:
>>> http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorial
>>>
>>>
>>>
>>> Hope this helps
>>> Hans-Rudolf
>>>
>>>
>>>
>>>
>>>
>>> On 07/16/2013 08:35 PM, Moritz Juchler wrote:
>>>
 Hello Ladies and Gentlemen,

 I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
 have to choose a bioinformatic pipeline management tool to find SNP's in
 genomes from hcc patients. My decision was made in favor of galaxy. I
 have a 64-bit openSuse 11.3 server.
 I have installed Galaxy locally, since we have a) very large files
 (>30GB per patient) and b) the data is protection sensitive. I kept
 close to 
 http://wiki.galaxyproject.org/**Admin/Get%20Galaxy
 Now I would like to run this bpipe pipeline:
 http://pastebin.com/sZd5vfdL
 And the first step is to align my genome to a _hg19 reference genome_

 which I have locally under /genedata/human_genome_GRCh37/**.

 trr@portalmoritz:~> ls -l /genedata/human_genome_GRCh37/
 total 8486312
 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa
 -rw-r--r-- 1 trr root   8591 2013-07-01 16:06 hg19.fa.amb
 -rw-r--r-- 1 trr root   4040 2013-07-01 16:06 hg19.fa.ann
 -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt
 -rw-r--r-- 1 trr root  784290318 2013-07-01 16:06 hg19.fa.pac
 -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa
 


 _bwa is installed and gives me:_


 trr@portalmoritz:~> bwa
 Program: bwa (alignment via Burrows-Wheeler transformation)
 Version: 0.7.5a-r405
 Contact: Heng Li mailto:l...@sanger.ac.uk>>



 Then I tried to follow this guide:
 http://wiki.galaxyproject.org/**Admin/NGS%20Local%20Setupto
  get the
 reference files and
 http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencies
 .

 This is my _$PATH_


 trr@portalmoritz:~> echo $PATH
 /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/**
 usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/**
 home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19


 _In the universe_wsgi.ini I changed:_


 tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir
 debug = False
 use_interactive = True
 library_import_dir = /genedata/
 allow_library_path_paste = True
 admin_users = ...


 This is m

[galaxy-dev] Cloudman - is it possible to still use depreciated AMIs ?

[Ravpreet Setia]

I tried launching an instance specifying "ami-da58aab3" as the AMI but I am 
unable to SSH or access Cloudman using the instance's URL.
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[galaxy-dev] Cloudman master cannot connect to volume at start-up

[Ravpreet Setia]

  *   This is what has been reported by the cluster status log:
  *
  *   20:01:14 - Master starting
  *   20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb: 
EC2ResponseError: 400 Bad RequestInvalidVolume.NotFoundThe volume 
'vol-91cfd1cb' does not exist.9179663c-c5ec-4e90-88ff-ecf606b5e9a6
  *   20:01:16 - Attempting to connect to a non-existent volume vol-91cfd1cb
  *   20:01:16 - Error processing filesystems in existing cluster 
configuration: 'NoneType' object has no attribute '__getitem__'
  *   20:01:16 - * Manager failed to start *

Any suggestions?
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Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome

[Moritz Juchler]

Hey,

with the "tool file" line I got it working :)
Thanks a lot. Could you answer the question regarding Tool Shed: "If I
would use Tool Shed, could I skip all these manual steps? Is the
installation of BWA with Tool Shed also this complicated or is it more
simle?"

Best
Moritz


On 17 July 2013 09:51, Moritz Juchler wrote:

> Hey,
>
> no thats correct I did not use Tool Shed. If I would use it, could I skip
> all these manual steps? Is the installation of BWA with Tool Shed also this
> complicated or is it more simle?
>
> How did you not follow my steps :) I wrote down everything clearly, at
> least thats what I was hoping.
>
> And no I didnt write this line "  />" Thats the first time, I am seeing this tutorial :( I will try this
> out right now
>
> Best
> Moritz
>
>
> On 17 July 2013 09:42, Hans-Rudolf Hotz  wrote:
>
>> Hi Moritz
>>
>> I am struggling to follow what exactly you have done. As far as I can
>> see, you did not use the toolshed (http://wiki.galaxyproject.**
>> org/Tool%20Shed ) to install
>> the BWA alinger tool, but did all manually?
>>
>> If so, have you added the following line:
>>
>>  
>>
>> to the "tool_conf.xml" file, and restarted Galaxy?
>>
>>
>> see also:
>> http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorial
>>
>>
>>
>> Hope this helps
>> Hans-Rudolf
>>
>>
>>
>>
>>
>> On 07/16/2013 08:35 PM, Moritz Juchler wrote:
>>
>>> Hello Ladies and Gentlemen,
>>>
>>> I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
>>> have to choose a bioinformatic pipeline management tool to find SNP's in
>>> genomes from hcc patients. My decision was made in favor of galaxy. I
>>> have a 64-bit openSuse 11.3 server.
>>> I have installed Galaxy locally, since we have a) very large files
>>> (>30GB per patient) and b) the data is protection sensitive. I kept
>>> close to 
>>> http://wiki.galaxyproject.org/**Admin/Get%20Galaxy
>>> Now I would like to run this bpipe pipeline:
>>> http://pastebin.com/sZd5vfdL
>>> And the first step is to align my genome to a _hg19 reference genome_
>>>
>>> which I have locally under /genedata/human_genome_GRCh37/**.
>>>
>>> trr@portalmoritz:~> ls -l /genedata/human_genome_GRCh37/
>>> total 8486312
>>> -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa
>>> -rw-r--r-- 1 trr root   8591 2013-07-01 16:06 hg19.fa.amb
>>> -rw-r--r-- 1 trr root   4040 2013-07-01 16:06 hg19.fa.ann
>>> -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt
>>> -rw-r--r-- 1 trr root  784290318 2013-07-01 16:06 hg19.fa.pac
>>> -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa
>>> 
>>>
>>>
>>> _bwa is installed and gives me:_
>>>
>>>
>>> trr@portalmoritz:~> bwa
>>> Program: bwa (alignment via Burrows-Wheeler transformation)
>>> Version: 0.7.5a-r405
>>> Contact: Heng Li mailto:l...@sanger.ac.uk>>
>>>
>>>
>>>
>>> Then I tried to follow this guide:
>>> http://wiki.galaxyproject.org/**Admin/NGS%20Local%20Setupto
>>>  get the
>>> reference files and
>>> http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencies
>>> .
>>>
>>> This is my _$PATH_
>>>
>>>
>>> trr@portalmoritz:~> echo $PATH
>>> /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/**
>>> usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/**
>>> home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19
>>>
>>>
>>> _In the universe_wsgi.ini I changed:_
>>>
>>>
>>> tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir
>>> debug = False
>>> use_interactive = True
>>> library_import_dir = /genedata/
>>> allow_library_path_paste = True
>>> admin_users = ...
>>>
>>>
>>> This is my _tool_dependency_dir:_
>>>
>>>
>>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa> ls -l
>>> total 4
>>> drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4
>>> lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default -> 0.7.4/
>>>
>>>
>>> This is the_version folder of bwa:_
>>>
>>>
>>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4>
>>> ls -l
>>> total 8
>>> drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin
>>> -rw-r--r-- 1 trr users   47 2013-07-16 14:22 env.sh
>>>
>>>
>>> This is the _content of env.sh:_
>>>
>>>
>>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4>
>>> cat env.sh
>>> PATH="/home/trr/bwa-0.7.5a/:$**PATH"
>>> export PATH
>>>
>>>
>>> And this is the _content of the bin folder:_
>>>
>>>
>>> trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4/bin>
>>> ls -l
>>> total 3896
>>> -rw-r--r-- 1 trr users   6098 2013-07-16 14:18 bamlite.c
>>> -rw-r--r-- 1 trr users   3124 2013-07-16 14:18 b

Re: [galaxy-dev] unable to display text output

[Hotz, Hans-Rudolf]

Hi Mark

Quick answer:  It could be an issue with your browser. Have you tried looking 
at your date with a different web browser and/or on a different machine?

Long answer: Could you please clarify, as I can't really follow your 
description of the problemyou say: it is working if you change the data 
format manually to 'txt', but it is not working if you specify it as 'txt' in 
the tool xml? And when you specify it as 'txt' in the tool xml do you get 
"format: txt," in the history display?



Regards, Hans-Rudolf


On Jul 22, 2013, at 3:27 PM, 
mailto:mark.r...@syngenta.com>>
 wrote:

Hi All

I’m trying to format one of the three outputs of my galaxy tool as plain text.  
Thus far no matter how I specify my output format in the tool xml file I have 
the same problem.  When I click the eye icon it opens a save dialog rather that 
displaying the text output in the central frame.  The preview shows the text 
output and if I follow through and save the output and open with wordpad it is 
fine.  Also if I edit the attributes of the output and change it to “txt” 
(which is one of the formats I had tried specifying in the xml)  it will render 
in the central frame but I would rather not have to do that.  Both of my other 
outputs (a vcf and a tab-delimited file) are rendered in the central frame 
properly.  How do I to fix this?

Thanks

Mark




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[galaxy-dev] Problem with tophat in local instance

[Rainy Luo]

Hi,all,
I am a beginner of Galaxy.Because I need to analyze large-scale deep-seq
data and the pubic Galaxy serve did not work out,I installed linux(the
first time to use linux) and set up the local galaxy instance in my
computer. It seemed everything worked fine until I tried to use Tophat to
align the reads to the reference genome.The problem is although I have
already downloaded the Refgenome from UCSC,when I use the Tophat,"select a
reference genome"option is empty.
is there anybody having similar problem?How to deal with it?
Thanks!

Rainy
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Re: [galaxy-dev] Adding files to a data library - genome option

[Carl Eberhard]

That's both a bug (should default to 'unspecified') and a usability issue
(sorting the genomes). I've added a card:
https://trello.com/c/Hr1JdeGq/1007-ui-bug-genome-selection-when-adding-library-data-files


On Thu, Jul 11, 2013 at 11:06 AM, Lionel Guy  wrote:

> Hi Galaxy-devs,
>
> When adding files to a data library (as admin), I have to choose the
> genome corresponding to my dataset, but the drop-down list is not sorted,
> making it a tad annoying to scroll. In addition, by default, the homIni20
> genome is selected, which seems a bit anthropocentric ;)
>
> I would suggest that the genome drop-down list has the same behavior as
> the one in the Upload File tool (i.e. sorted alphabetically, with
> "unspecified" as the default value).
>
> Not sure this is a bug or even worth a Trello card, so I post it here. I'd
> be happy to fill in a Trello card if requested.
>
> Cheers,
>
> Lionel
> __**_
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>  
> http://galaxyproject.org/**search/mailinglists/
>
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Re: [galaxy-dev] workflow: default parameters

[James Taylor]

Not currently possible, but it shouldn't be too difficult to make
work. Please file a Trello card.

On Tue, Jul 9, 2013 at 11:36 AM, Keilwagen, Jens
 wrote:
> when building workflows we can choose for each parameter whether to 'set at 
> runtime' or to 'set in advance' (when creating or editing the workflow). We 
> are looking for a possiblity to set a default value that is used (only) for 
> the workflow, i.e., we like to specify a value that might be used by most 
> users, but might be altered by expert users. This value might be different 
> from the default value of the corresponding tool. So far, we did not find any 
> possiblity.


--
James Taylor, Assistant Professor, Biology/CS, Emory University

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Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome

[Peter Cock]

On Mon, Jul 22, 2013 at 10:40 AM, Moritz Juchler
 wrote:
> Hey,
>
> now I am having a new problem: Convert SAM to BAM
> Tool execution generated the following error message:
>
> [samopen] SAM header is present: 93 sequences.
> Parse error at line 106: sequence and quality are inconsistent
> /bin/sh: line 1: 27934 Aborted samtools view -bS
> "/home/trr/galaxy-dist/database/files/000/dataset_17.dat" >
> "/tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam"

That's bad.

> The tool produced the following additional output:
>
> [bam_header_read] EOF marker is absent. The input is probably truncated.
>
> (should I make a new post out of this?)

Which version of samtools? There is a bug in the
currently release where that warning is a false alarm:
https://github.com/samtools/samtools/issues/18

Peter
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Re: [galaxy-dev] ToolShed preview lacking controls

[Peter Cock]

On Mon, Jul 22, 2013 at 3:03 PM, Greg Von Kuster  wrote:
> Hi Peter,
>
> This is a known issue - there is a Trello card for it here:
>
> https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action
>
> Thanks,
>
> Greg Von Kuster

Thanks Greg - I've subscribed & voted for that issue :)

Peter
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Re: [galaxy-dev] ToolShed preview lacking controls

[Greg Von Kuster]

Hi Peter,

This is a known issue - there is a Trello card for it here:

https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action

Thanks,

Greg Von Kuster

On Jul 22, 2013, at 9:12 AM, Peter Cock  wrote:

> HI all,
> 
> I just had a query about some 'missing' functionality in one of my
> tools, which is handled by a parameter which doesn't get shown
> on the preview shown in the Tool Shed - perhaps because it is
> inside a conditional?
> 
> 
> 
> Both positive matches (ID on list) and negative
> matches (ID not on list), as two files
> Just positive matches (ID on list), as a single
> file
> Just negative matches (ID not on list), as a
> single file
> 
> 
> 
> 
> 
> 
> 
> Ideally the ToolShed preview would show the dropdown combo
> box allowing you to pick both files, positive only, or negative only:
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
> 
> Is this a known limitation? Is there a Trello card I should follow?
> 
> Thanks,
> 
> Peter
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> 
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Re: [galaxy-dev] Manual modifications to integrated_tool_panel.xml?

[Björn Grüning]

Hi Dan,

> Hi, Galaxy Developers,
> 
> I have what I believe to be a basic question/problem with respect to making 
> modifications to the integrated_tool_panel.xml (and or tool_conf.xml).  Our 
> Galaxy deployment does have some custom additions made to these files (I did 
> not make these modifications so I am not 100% certain at this point whether 
> or not the modifications to integrated_tool_panel.xml were manual or 
> propagated from elsewhere) , and everything seems to work alright, although I 
> do have a problem that I am having somewhat of a difficult time resolving.  
> Before ask my question, I wanted to confirm my understanding of the wiki page 
> http://wiki.galaxyproject.org/GalaxyToolPanel.  I was hoping that somebody 
> could validate the following statements;
> 
> 1) The only thing that a human being should really ever change in the file 
> "integrated_tool_panel.xml" is the ordering of the groupings (I believe I 
> read on the developer mailing list that it was acceptable to delete sections 
> from here as well, although I am not attempting to validate this at this 
> time).
> 2) That for all intensive purposes, the integrated_tool_panel.xml should be 
> generated automatically from the files specified in the  "tool_config_file" 
> configuration directive in universe_wsgi.ini.
> 3) That it is perfectly to acceptable to make manual modifications to XML 
> files supplied in the configuration directive "tool_config_file" in the 
> universe_wsgi.ini, or add any number additional XML files to this list 
> (presumably I wouldn't want to make too many manual changes to the 
> shed_tool_conf.xml file, I'm referring to the other XML files, not this one).
> 
> The reason I am asking this question is a fairly simple one; every now and 
> then, it appears that new tools are released when new versions of Galaxy are 
> released (i.e. a slightly different default toolset is offered, and thus tool 
> panel and or tool configuration files are generated when the new version of 
> Galaxy is started, at least if I do a fresh install).  It appears to me based 
> on some very basic testing that once a manual modification to the 
> tool_conf.xml is made,  that the next time a pull for an update is run and 
> Galaxy is restarted, that these files remain as-is; basically, what appears 
> to be happening is that we are running a new version of Galaxy with what 
> seems to be an out-of-date integrated_tool_panel.xml, at least in terms of 
> the tools that are configured as part of the default install; this, in a 
> nutshell, is the fundamental problem I am currently dealing with.
> 
> Here is what I'm thinking is the "correct" way to solve my problem;
> 1) Since we are manually modifying the tools_conf.xml, It seems to me that we 
> are kind of shooting ourselves in the foot in terms of our ability to delete 
> this file and have Galaxy update it when we do an upgrade .  Based on what I 
> know I feel that we should do is take all of our custom tools modifications 
> and put them in a separate file called uofc_custom_tools.xml, and then add 
> that to "tool_config_file" to abstract away our custom tool configurations 
> from the default tool_conf.xml.
> 2) When we upgrade galaxy, delete the tools_conf.xml, and when galaxy starts, 
> let it replace this file with the default from the current changeset.
> 3) As long as we didn't need to do any manually reordering of elements in the 
> integrated_tool_panel.xml, just delete the integrated_tool_panel.xml, and 
> allow it to be manually re-generated from tool_conf.xml and 
> uofc_custom_tools.xml.
> 
> Does this solution sound reasonable? 

Yes :)! Having local modifications in a separate file makes totally
sense! 
Step 2. is not necessary, imho, you can also merge both files
tools_conf.xml and tools_conf.xml.sample if you like.


>  I would be very grateful on any insight anybody could provide in the best 
> way to address this problem.  I wish you a wonderful day.

You too!
Bjoern

> Dan Sullivan
> ___
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> and other Galaxy lists, please use the interface at:
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[galaxy-dev] unable to display text output

[mark.rose]

Hi All

I'm trying to format one of the three outputs of my galaxy tool as plain text.  
Thus far no matter how I specify my output format in the tool xml file I have 
the same problem.  When I click the eye icon it opens a save dialog rather that 
displaying the text output in the central frame.  The preview shows the text 
output and if I follow through and save the output and open with wordpad it is 
fine.  Also if I edit the attributes of the output and change it to "txt" 
(which is one of the formats I had tried specifying in the xml)  it will render 
in the central frame but I would rather not have to do that.  Both of my other 
outputs (a vcf and a tab-delimited file) are rendered in the central frame 
properly.  How do I to fix this?

Thanks

Mark




This message may contain confidential information. If you are not the 
designated recipient, please notify the sender immediately, and delete the 
original and any copies. Any use of the message by you is prohibited. 
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[galaxy-dev] ToolShed preview lacking controls

[Peter Cock]

HI all,

I just had a query about some 'missing' functionality in one of my
tools, which is handled by a parameter which doesn't get shown
on the preview shown in the Tool Shed - perhaps because it is
inside a conditional?



Both positive matches (ID on list) and negative
matches (ID not on list), as two files
Just positive matches (ID on list), as a single
file
Just negative matches (ID not on list), as a
single file







Ideally the ToolShed preview would show the dropdown combo
box allowing you to pick both files, positive only, or negative only:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id

Is this a known limitation? Is there a Trello card I should follow?

Thanks,

Peter
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Re: [galaxy-dev] ProFTPD integration with Galaxy

[Federico Zambelli]

I noticed the errors in the SUBSTRING length too and I modified my 
configuration file accordingly but still not able to authenticate :(


F.

Il 22/07/13 05.40, TerryYeh@NARL ha scritto:

Dear All,

 I am having a similar problem too. I followed the config
setting provide by Mr. Perez and modified some possible error. I still
cannot login my ftp server. Following is my proftpd.conf. Please help me
to figure out the problem. Thanks a lot!!

# This is a basic ProFTPD configuration file (rename it to

# 'proftpd.conf' for actual use.  It establishes a single server

# and a single anonymous login.  It assumes that you have a user/group

# "nobody" and "ftp" for normal operation and anon.

ServerName "ProFTPD Default Installation"

ServerType standalone

DefaultServer on

# Port 21 is the standard FTP port

Port 2121

# Don't use IPv6 support by default.

UseIPv6 off

# Umask 022 is a good standard umask to prevent new dirs and files

# from being group and world writable.

Umask 022

# To prevent DoS attacks, set the maximum number of child processes

# to 30.  If you need to allow more than 30 concurrent connections

# at once, simply increase this value.  Note that this ONLY works

# in standalone mode, in inetd mode you should use an inetd server

# that allows you to limit maximum number of processes per service

# (such as xinetd).

MaxInstances30

# Set the user and group under which the server will run.

User username

Group groupname

PassivePorts 4 40999

# To cause every FTP user to be "jailed" (chrooted) into their home

# directory, uncomment this line.

#DefaultRoot ~

CreateHome on dirmode 700

# Normally, we want files to be overwriteable.

AllowOverwrite on

AllowStoreRestart on

# Bar use of SITE CHMOD by default



   DenyAll





   DenyAll





   LoadModule mod_sql.c

   LoadModule mod_sql_passwd.c

   LoadModule mod_sql_postgres.c



SQLLogFile /pkg/biology/galaxy/proftpd/log/proftpd-sql-local

##

ServerLog /pkg/biology/galaxy/proftpd/var/proftpd-server.log

SystemLog /pkg/biology/galaxy/proftpd/var/proftpd-system.log

#AuthPAMConfig ftp

#AuthOrder mod_auth_pam.c* mod_auth_unix.c

# Do not authenticate against real (system) users

AuthPAM off

#AuthOrder mod_sql.c

# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1

SQLPasswordEngine on

SQLPasswordEncoding hex

# Set up mod_sql to authenticate against the Galaxy database

SQLEngine on

SQLBackend postgres

SQLConnectInfo galaxy@localhost username password

SQLAuthTypes SHA1 SHA256 pbkdf2

SQLPasswordPBKDF2 SHA256 1 24

SQLAuthenticate users

# An empty directory in case chroot fails

#SQLDefaultHomedir /var/opt/local/proftpd

# Define a custom query for lookup that returns a passwd-like entry.
UID and GID should match your Galaxy user.

SQLUserInfo custom:/LookupGalaxyUser

SQLPasswordUserSalt sql:/GetUserSalt

#SQLNamedQuery LookupGalaxyUser  SELECT
"email,password,'12345','1234','/home/username/galaxyftp/%U','/bin/bash'
FROM galaxy_user WHERE email='%U'"

SQLNamedQuery LookupGalaxyUser  SELECT "email, (CASE WHEN
substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from
38 for 32) ELSE password END) AS
password,'12345','1234','/home/username/galaxyftp/%U','/bin/bash' FROM
galaxy_user WHERE email='%U'"

SQLNamedQueryGetUserSalt SELECT "(CASE WHEN SUBSTRING (password from
1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS
salt FROM galaxy_user WHERE email='%U'"

I still get the message of authentication failed.

2013-07-22 11:07:29,590 mod_sql/4.3[8124]: checking password using
SQLAuthType 'sha1'

2013-07-22 11:07:29,590 mod_sql/4.3[8124]: 'sha1' SQLAuthType handler
reports failure

2013-07-22 11:07:29,590 mod_sql/4.3[8124]: checking password using
SQLAuthType 'sha256'

2013-07-22 11:07:29,590 mod_sql/4.3[8124]: 'sha256' SQLAuthType handler
reports failure

2013-07-22 11:07:29,590 mod_sql/4.3[8124]: checking password using
SQLAuthType 'pbkdf2'

2013-07-22 11:07:29,619 mod_sql/4.3[8124]: 'pbkdf2' SQLAuthType handler
reports failure

Any suggestion on my configuration file, Thanks.



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--

Federico Zambelli, Ph.D.
Bioinformatics, Evolution and Comparative Genomics Lab
Dept. of Biosciences
University of Milano - Italy

What can be asserted without proof can be dismissed without proof.

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Re: [galaxy-dev] ProFTPD integration with Galaxy

[Rémy Dernat]

Sorry, I didn't see the recent changes...


2013/7/22 Rémy Dernat 

> Hi,
>
> 1/ Do you know who is your (FTP) galaxy user ? The proftpd daemon should
> run whith this user (be carefull to permissions).
> 2/ Did you try a simpler way to authenticate to your postgresql server ?
> I mean, you choose to add some parameter as "SQLPasswordPBKDF2" or 
> "SQLPasswordUserSalt".
> You should know what kind of algorithm is used to encrypt password on your
> postgres server and then use it...
> Follow this tutorial :
> http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP
>
> If it works, then add 'salt' method if you wish, or other algorithm/method
> to encrypt password...
>
> Regards
>
>
> 2013/7/22 TerryYeh@NARL 
>
>>  Dear All,
>>
>> I am having a similar problem too. I followed the config setting
>> provide by Mr. Perez and modified some possible error. I still cannot login
>> my ftp server. Following is my proftpd.conf. Please help me to figure out
>> the problem. Thanks a lot!!
>>
>> ** **
>>
>> # This is a basic ProFTPD configuration file (rename it to
>>
>> # 'proftpd.conf' for actual use.  It establishes a single server
>>
>> # and a single anonymous login.  It assumes that you have a user/group***
>> *
>>
>> # "nobody" and "ftp" for normal operation and anon.
>>
>> ** **
>>
>> ServerName  "ProFTPD Default Installation"
>>
>> ServerType  standalone
>>
>> DefaultServer   on
>>
>> ** **
>>
>> # Port 21 is the standard FTP port
>>
>> Port2121
>>
>> ** **
>>
>> # Don't use IPv6 support by default.
>>
>> UseIPv6 off
>>
>> ** **
>>
>> # Umask 022 is a good standard umask to prevent new dirs and files
>>
>> # from being group and world writable.
>>
>> Umask   022
>>
>> ** **
>>
>> # To prevent DoS attacks, set the maximum number of child processes
>>
>> # to 30.  If you need to allow more than 30 concurrent connections
>>
>> # at once, simply increase this value.  Note that this ONLY works
>>
>> # in standalone mode, in inetd mode you should use an inetd server
>>
>> # that allows you to limit maximum number of processes per service
>>
>> # (such as xinetd).
>>
>> MaxInstances30
>>
>> ** **
>>
>> # Set the user and group under which the server will run.
>>
>> Userusername
>>
>> Group   groupname
>>
>> ** **
>>
>> ** **
>>
>> PassivePorts4 40999
>>
>> # To cause every FTP user to be "jailed" (chrooted) into their home
>>
>> # directory, uncomment this line.
>>
>> #DefaultRoot ~
>>
>> ** **
>>
>> CreateHome  on dirmode 700
>>
>> ** **
>>
>> # Normally, we want files to be overwriteable.
>>
>> AllowOverwrite  on
>>
>> ** **
>>
>> AllowStoreRestart   on
>>
>> ** **
>>
>> ** **
>>
>> # Bar use of SITE CHMOD by default
>>
>> 
>>
>>   DenyAll
>>
>> 
>>
>> ** **
>>
>> 
>>
>>   DenyAll
>>
>> 
>>
>> ** **
>>
>> ** **
>>
>> 
>>
>>   LoadModule mod_sql.c
>>
>>   LoadModule mod_sql_passwd.c
>>
>>   LoadModule mod_sql_postgres.c
>>
>> 
>>
>> ** **
>>
>> SQLLogFile /pkg/biology/galaxy/proftpd/log/proftpd-sql-local
>>
>> ** **
>>
>> ##
>>
>> ** **
>>
>> ServerLog /pkg/biology/galaxy/proftpd/var/proftpd-server.log
>>
>> SystemLog /pkg/biology/galaxy/proftpd/var/proftpd-system.log
>>
>> ** **
>>
>> ** **
>>
>> #AuthPAMConfig ftp
>>
>> #AuthOrder mod_auth_pam.c* mod_auth_unix.c
>>
>> ** **
>>
>> ** **
>>
>> # Do not authenticate against real (system) users
>>
>> AuthPAM off
>>
>> #AuthOrder   mod_sql.c
>>
>> ** **
>>
>> ** **
>>
>> # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded
>> SHA1
>>
>> SQLPasswordEngine   on
>>
>> SQLPasswordEncoding hex
>>
>> ** **
>>
>> # Set up mod_sql to authenticate against the Galaxy database
>>
>> SQLEngine   on
>>
>> SQLBackend  postgres
>>
>> SQLConnectInfo  galaxy@localhost username password
>>
>> SQLAuthTypesSHA1 SHA256 pbkdf2
>>
>> SQLPasswordPBKDF2   SHA256 1 24
>>
>> ** **
>>
>> SQLAuthenticate users
>>
>> ** **
>>
>> ** **
>>
>> # An empty directory in case chroot fails
>>
>> #SQLDefaultHomedir   /var/opt/local/proftpd
>>
>> ** **
>>
>> # Define a custom query for lookup that returns a passwd-like entry.  UID
>> and GID should match your Galaxy user.
>>
>> ** **
>>
>> SQLUserInfo custom:/LookupGalaxyUser
>>
>> SQLPasswordUserSalt sql:/GetUserSalt
>>
>> ** **
>>
>> #SQLNamedQuery   LookupGalaxyUser  SELECT
>> "email,password,'12345

[galaxy-dev] Manual modifications to integrated_tool_panel.xml?

[Dan Sullivan]

Hi, Galaxy Developers,

I have what I believe to be a basic question/problem with respect to making 
modifications to the integrated_tool_panel.xml (and or tool_conf.xml).  Our 
Galaxy deployment does have some custom additions made to these files (I did 
not make these modifications so I am not 100% certain at this point whether or 
not the modifications to integrated_tool_panel.xml were manual or propagated 
from elsewhere) , and everything seems to work alright, although I do have a 
problem that I am having somewhat of a difficult time resolving.  Before ask my 
question, I wanted to confirm my understanding of the wiki page 
http://wiki.galaxyproject.org/GalaxyToolPanel.  I was hoping that somebody 
could validate the following statements;

1) The only thing that a human being should really ever change in the file 
"integrated_tool_panel.xml" is the ordering of the groupings (I believe I read 
on the developer mailing list that it was acceptable to delete sections from 
here as well, although I am not attempting to validate this at this time).
2) That for all intensive purposes, the integrated_tool_panel.xml should be 
generated automatically from the files specified in the  "tool_config_file" 
configuration directive in universe_wsgi.ini.
3) That it is perfectly to acceptable to make manual modifications to XML files 
supplied in the configuration directive "tool_config_file" in the 
universe_wsgi.ini, or add any number additional XML files to this list 
(presumably I wouldn't want to make too many manual changes to the 
shed_tool_conf.xml file, I'm referring to the other XML files, not this one).

The reason I am asking this question is a fairly simple one; every now and 
then, it appears that new tools are released when new versions of Galaxy are 
released (i.e. a slightly different default toolset is offered, and thus tool 
panel and or tool configuration files are generated when the new version of 
Galaxy is started, at least if I do a fresh install).  It appears to me based 
on some very basic testing that once a manual modification to the tool_conf.xml 
is made,  that the next time a pull for an update is run and Galaxy is 
restarted, that these files remain as-is; basically, what appears to be 
happening is that we are running a new version of Galaxy with what seems to be 
an out-of-date integrated_tool_panel.xml, at least in terms of the tools that 
are configured as part of the default install; this, in a nutshell, is the 
fundamental problem I am currently dealing with.

Here is what I'm thinking is the "correct" way to solve my problem;
1) Since we are manually modifying the tools_conf.xml, It seems to me that we 
are kind of shooting ourselves in the foot in terms of our ability to delete 
this file and have Galaxy update it when we do an upgrade .  Based on what I 
know I feel that we should do is take all of our custom tools modifications and 
put them in a separate file called uofc_custom_tools.xml, and then add that to 
"tool_config_file" to abstract away our custom tool configurations from the 
default tool_conf.xml.
2) When we upgrade galaxy, delete the tools_conf.xml, and when galaxy starts, 
let it replace this file with the default from the current changeset.
3) As long as we didn't need to do any manually reordering of elements in the 
integrated_tool_panel.xml, just delete the integrated_tool_panel.xml, and allow 
it to be manually re-generated from tool_conf.xml and uofc_custom_tools.xml.

Does this solution sound reasonable?  I would be very grateful on any insight 
anybody could provide in the best way to address this problem.  I wish you a 
wonderful day.

Dan Sullivan
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Re: [galaxy-dev] ProFTPD integration with Galaxy

[Rémy Dernat]

Hi,

1/ Do you know who is your (FTP) galaxy user ? The proftpd daemon should
run whith this user (be carefull to permissions).
2/ Did you try a simpler way to authenticate to your postgresql server ?
I mean, you choose to add some parameter as "SQLPasswordPBKDF2" or
"SQLPasswordUserSalt".
You should know what kind of algorithm is used to encrypt password on your
postgres server and then use it...
Follow this tutorial :
http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP

If it works, then add 'salt' method if you wish, or other algorithm/method
to encrypt password...

Regards


2013/7/22 TerryYeh@NARL 

>  Dear All,
>
> I am having a similar problem too. I followed the config setting
> provide by Mr. Perez and modified some possible error. I still cannot login
> my ftp server. Following is my proftpd.conf. Please help me to figure out
> the problem. Thanks a lot!!
>
> ** **
>
> # This is a basic ProFTPD configuration file (rename it to
>
> # 'proftpd.conf' for actual use.  It establishes a single server
>
> # and a single anonymous login.  It assumes that you have a user/group
>
> # "nobody" and "ftp" for normal operation and anon.
>
> ** **
>
> ServerName  "ProFTPD Default Installation"
>
> ServerType  standalone
>
> DefaultServer   on
>
> ** **
>
> # Port 21 is the standard FTP port
>
> Port2121
>
> ** **
>
> # Don't use IPv6 support by default.
>
> UseIPv6 off
>
> ** **
>
> # Umask 022 is a good standard umask to prevent new dirs and files
>
> # from being group and world writable.
>
> Umask   022
>
> ** **
>
> # To prevent DoS attacks, set the maximum number of child processes
>
> # to 30.  If you need to allow more than 30 concurrent connections
>
> # at once, simply increase this value.  Note that this ONLY works
>
> # in standalone mode, in inetd mode you should use an inetd server
>
> # that allows you to limit maximum number of processes per service
>
> # (such as xinetd).
>
> MaxInstances30
>
> ** **
>
> # Set the user and group under which the server will run.
>
> Userusername
>
> Group   groupname
>
> ** **
>
> ** **
>
> PassivePorts4 40999
>
> # To cause every FTP user to be "jailed" (chrooted) into their home
>
> # directory, uncomment this line.
>
> #DefaultRoot ~
>
> ** **
>
> CreateHome  on dirmode 700
>
> ** **
>
> # Normally, we want files to be overwriteable.
>
> AllowOverwrite  on
>
> ** **
>
> AllowStoreRestart   on
>
> ** **
>
> ** **
>
> # Bar use of SITE CHMOD by default
>
> 
>
>   DenyAll
>
> 
>
> ** **
>
> 
>
>   DenyAll
>
> 
>
> ** **
>
> ** **
>
> 
>
>   LoadModule mod_sql.c
>
>   LoadModule mod_sql_passwd.c
>
>   LoadModule mod_sql_postgres.c
>
> 
>
> ** **
>
> SQLLogFile /pkg/biology/galaxy/proftpd/log/proftpd-sql-local
>
> ** **
>
> ##
>
> ** **
>
> ServerLog /pkg/biology/galaxy/proftpd/var/proftpd-server.log
>
> SystemLog /pkg/biology/galaxy/proftpd/var/proftpd-system.log
>
> ** **
>
> ** **
>
> #AuthPAMConfig ftp
>
> #AuthOrder mod_auth_pam.c* mod_auth_unix.c
>
> ** **
>
> ** **
>
> # Do not authenticate against real (system) users
>
> AuthPAM off
>
> #AuthOrder   mod_sql.c
>
> ** **
>
> ** **
>
> # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
> 
>
> SQLPasswordEngine   on
>
> SQLPasswordEncoding hex
>
> ** **
>
> # Set up mod_sql to authenticate against the Galaxy database
>
> SQLEngine   on
>
> SQLBackend  postgres
>
> SQLConnectInfo  galaxy@localhost username password
>
> SQLAuthTypesSHA1 SHA256 pbkdf2
>
> SQLPasswordPBKDF2   SHA256 1 24
>
> ** **
>
> SQLAuthenticate users
>
> ** **
>
> ** **
>
> # An empty directory in case chroot fails
>
> #SQLDefaultHomedir   /var/opt/local/proftpd
>
> ** **
>
> # Define a custom query for lookup that returns a passwd-like entry.  UID
> and GID should match your Galaxy user.
>
> ** **
>
> SQLUserInfo custom:/LookupGalaxyUser
>
> SQLPasswordUserSalt sql:/GetUserSalt
>
> ** **
>
> #SQLNamedQuery   LookupGalaxyUser  SELECT
> "email,password,'12345','1234','/home/username/galaxyftp/%U','/bin/bash'
> FROM galaxy_user WHERE email='%U'"
>
> SQLNamedQueryLookupGalaxyUser  SELECT "email, (CASE WHEN
> substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38
> for 32) ELSE password END) AS
> password,'12345','1234','/home/username/galaxyftp/