Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

[Peter Cock]

On Wed, May 22, 2013 at 9:26 PM, Peter Cock  wrote:
>
> On Mon, May 20, 2013 at 3:05 PM, Peter Cock wrote:
> > On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster wrote:
> >> Peter wrote:
> >> I've copied the blast_datatypes from the main tool shed to the test
> >> tool shed with all history in tact.  See
> >>
> >> http://testtoolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
> >>
> >
> > Great, I'm trying that now here:
> >
> > http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/9ef0d4ecb9d5
> >
> > http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c
> >
> > http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180
>
> Hi Greg (& Dave),
>
> Thanks for Dave for fixing the missing test results issue,
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014791.html
>
> I can now see the effect the dependency change had -
> unfortunately the blast_datatypes install seems to be
> unsuccessful, but I am not seeing a helpful error from
> the Tool Shed tests.

Hi Greg,

Something is still amiss with this dependency and/or the Tool
Shed display. These two are currently listed under "Latest revision:
installation errors" but don't show any errors or test failures:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/482b7f4d3587

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/c4f503750a44

On other hand, this third tool with the blast_datatypes dependency
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
fails with a known issue:
https://trello.com/card/-/506338ce32ae458f6d15e4b3/801

I'm not seeing any similar issue with the ncbi_blast_plus suite:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/bb81d3afa28d

Regards,

Peter
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Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

[Peter Cock]

On Fri, May 24, 2013 at 11:18 AM, Peter Cock  wrote:
>
> Hi Greg,
>
> Something is still amiss with this dependency and/or the Tool
> Shed display. These two are currently listed under "Latest revision:
> installation errors" but don't show any errors or test failures:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/482b7f4d3587
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/c4f503750a44
>
> ...

Correction - clinod doesn't depend on blast_datatypes so whatever
is going wrong is likely a more general tool installation failure.

Peter
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Re: [galaxy-dev] Displaying genomic sequences in Trackster

[menorca]

> > 
> > On Apr 18, 2012, at 9:05 AM, 
Naharajan Lakshmanaperumal wrote:
> > 
> >> Dear all,
> >> We have our own galaxy instance and the idea is to have
 trackster enabled for users to be 
able to visualize NGS mapping. We were able to configure 
trackster in our instance and the visualization works fine. 
> >> We have two questions regarding trackster:
> >> 1) We can't display genomic sequences in trackster. 
As per the tutorial, we set the location of 
the .2bit
> file in the twobit.loc file for the trackster to be able 
to display the genomic sequence but for 
some reason
> it doesn't display it. 

 Hello!
I am trying to enable Trackster on our local galaxy to 
visualize the mapping results.
But, so far, it is not working.
Is the twobit.loc file necessary for using Trackster? or is it just optional?

Best regards,
Menorca

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[galaxy-dev] Problem to download mercurial egg

[Marc DELOGER]

Hello,

I tried to download several times the several egg on these following 
mirrors but the download is always blocked near 50%...I asked several 
different people and they all have the same problem :


http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg 



http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg 



Thank you in advance,

Marc DELOGER
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Re: [galaxy-dev] Displaying genomic sequences in Trackster

[Jeremy Goecks]

> Hello!
> I am trying to enable Trackster on our local galaxy to 
> visualize the mapping results.
> But, so far, it is not working.
> Is the twobit.loc file necessary for using Trackster? or is it just optional?
> 
> Best regards,
> Menorca

Twobit files, configured via twobit.loc, are optional. Here is a page that 
lists all the steps required to get Galaxy genome visualizations (including 
Trackster) working: http://wiki.galaxyproject.org/Visualization%20Setup

Let us know if you run into any problems or have questions.

Thanks,
J.


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Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

[Dave Bouvier]

Peter,

The issue was the same as before, an earlier repository in the list took 
longer than 1800 seconds to compile tool dependencies, so the testing 
framework canceled the install and test process. I've added that 
repository to the exclude list, and implemented a framework to install 
and test a single repository in the same environment as is used for the 
nightly test runs. I have also run that framework on the clinod 
repository, and you should now see relevant test results.


   --Dave B.

On 5/24/13 06:21:01.000, Peter Cock wrote:

On Fri, May 24, 2013 at 11:18 AM, Peter Cock  wrote:


Hi Greg,

Something is still amiss with this dependency and/or the Tool
Shed display. These two are currently listed under "Latest revision:
installation errors" but don't show any errors or test failures:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/482b7f4d3587

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/c4f503750a44

...


Correction - clinod doesn't depend on blast_datatypes so whatever
is going wrong is likely a more general tool installation failure.

Peter
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Re: [galaxy-dev] Is there a way through the API to know when a file has completed the upload process?

[Thon de Boer]

It seems that there are not a lot of people using/know about the API since
all my questions about the API here go unanswered, but I am happy to report
that I don't actually need to know if the upload has finished, since it
seems you can start a workflow with a dataset that is still being
uploaded.You can't do this in the UI but it seems you CAN do it through the
API, so that is a relief..

 

Now if only the API allowed us to pass parameters to a workflow in the same
way we can do this in the API, I am set and I can use Galaxy as a workflow
engine through the API..

 

Regards,

 

Thon

 

Thon deBoer Ph.D., Bioinformatics Guru 
California, USA |p: +1 (650) 799-6839  |m:  thondeb...@me.com
 

 

From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Anthonius deBoer
Sent: Tuesday, May 21, 2013 6:24 PM
To: Galaxy-dev Galaxy-dev
Subject: [galaxy-dev] Is there a way through the API to know when a file has
completed the upload process?

 

Hi,

 

I am trying to use the API to upload a file and since the upload can take a
long time (see my previous post) I need to check if the upload has completed
so I know I can start a workflow (or can I start a workflow even when the
file is still in the "queued" state?)...

 

I have successfully used the examples from this page:

 

http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.h
tml

 

and can easily upload a file, but I cannot seem to learn the state of the
file...

The upload process I used, returned a bunch of attributes, such as:

 

{'ldda_id': '049d723a33542847', 'misc_blurb': None, 'name':
'7_101_1_ACTTGA_R1.fastq', 'data_type': 'fastq', 'file_name':
'/mnt/ngs/analysis/tdeboer/PROJECTS/STAGING/SEQUENCER07/130207_SN7001380_010
1_AD1H7GACXX/fastq/7_101_1_ACTTGA_R1.fastq', 'uploaded_by':
'tdeb...@genomichealth.com', 'metadata_sequences': None, 'template_data':
{}, 'genome_build': 'hg19', 'model_class': 'LibraryDataset', 'misc_info':
None, 'file_size': 6410080411, 'metadata_data_lines': None, 'message': '',
'id': '049d723a33542847', 'date_uploaded': '2013-05-22T00:50:50.474318',
'metadata_dbkey': 'hg19'}

 

But none of those tell me if the upload has succeeded or not...

 

Is there a way to retrieve the state of an uploaded file once I have
uploaded a file through the API?

 

thanks


Thon

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[galaxy-dev] Problem to download mercurial egg

[Jennifer Jackson]

Moving the question over to development list
http://wiki.galaxyproject.org/MailingLists

 Original Message 
Subject:[galaxy-user] Problem to download mercurial egg
Date:   Fri, 24 May 2013 14:17:11 +0200
From:   Marc DELOGER 
To: 



Hello,

I tried to download several times the several egg on these following 
mirrors but the download is always blocked near 50%...I asked several 
different people and they all have the same problem :


http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg 



http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg 



Thank you in advance,

Marc DELOGER

--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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Re: [galaxy-dev] populating the pull-down menu: reference genomes (built-in index)

[Jennifer Jackson]

Hello Jeannette,

Data is available from our rsync server, as explained here:
http://wiki.galaxyproject.org/Admin/Data%20Integration
See "Get the data"

If you need to make indexes that we do not have, each tool's original 
documentation will have general instructions and the Galaxy .loc file 
has instructions for how to configure so that these are usable by tools. 
We also give specific instructions for many here:

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Hopefully this helps,

Jen
Galaxy team

On 5/22/13 10:45 AM, Staheli, Jeannette wrote:


Hi,

We are trying to put a few reference genomes into the built-in index 
for bwa, bowtie, bowtie2 and tophat.  For the human hg19 we can find 
those.  However, we also like to upload the Rhesus macaque genome and 
haven't been able to find an indexed version at NCBI or other places.


Are other genomes pre-indexed for these applications somewhere?

How do those files look like exactly (extensions, number of files 
needed, etc.)?


How would we index the Rhesus genome for the above mappers if they are 
not available in an indexed form?


Thank you,

Jeannette

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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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Re: [galaxy-dev] Problem about main.g2.bx.psu.edu is taking too long to respond.

[Jennifer Jackson]

Hi Chureerat,

We emailed about this yesterday, but for others who may have noticed a 
few interruptions, I wanted to reply on this.


There were some known, intermittent, peak usage times earlier in the 
week, but these should be mostly resolve. Galaxy is still busy, so if 
this does come up again, just wait a few minutes, then try the query again.


Take care,

Jen
Galaxy team

On 5/23/13 7:04 AM, จุรีรัตน์ โพธิ์แก้ว wrote:

Dear Galaxy team,

I have problem with my galaxy because I can 't check my data.
I refresh my page several time but it keep report the connection has 
timed out.


Please let me know what should I do to fix this problem.

Thanks,
Chureerat


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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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Re: [galaxy-dev] Problem with ftp connexion to Galaxy

[Jennifer Jackson]

Hello,

New accounts (created this week) cannot FTP at this time. We hope to 
have this resolved soon. Please feel free to contact us for an update if 
this is still a problem by next Friday.


Our apologies for the inconvenience,

Jen
Galaxy team

On 5/22/13 6:34 AM, Fabrice BESNARD wrote:

Hello,

I am a new Galaxy User.
I am definitely not an expert in informatics, so my questions may sound
silly to you... I apologize if it is the case!
Anyway, I cound not establish a ftp connexion to Galaxy through Filezilla,
and the error message suggests that it comes from an incorrect password to
Galaxy.

Here is the messages displayed by Filezilla (french version) while trying
to connnect:

Statut :Résolution de l'adresse de main.g2.bx.psu.edu
Statut :Connexion à 128.118.250.4:21...
Statut :Connexion établie, attente du message d'accueil...
Réponse :   220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP)
[:::128.118.250.4]
Commande :  USER fbesn...@biologie.ens.fr
Réponse :   331 Password required for fbesn...@biologie.ens.fr
Commande :  PASS ***
Réponse :   530 Login incorrect.
Erreur :Erreur critique
Erreur :Impossible d'établir une connexion au serveur

I was puzzled by this error message, because I do connect as user in the
Galaxy website. As recommended, I use the SAME login (=email
adress)/Password in both Galaxy login page and filezilla.
I tried to reset my password and connect again: I could connect directly
to the web site, but I still failed establishing a connexion via
filezilla.

I just created an account yesterday to Galaxy (Tuesday, 21th of May 2013).
Maybe I should just wait a little bit for a synchronization of the user
connexion parameters, should I?

Moreover, my Filezilla is working with other ftp server, so that I think
we can exclude that the problem comes from there.

I extensively looked for similar trouble reports on internet (googling
with other terms "530 Login incorrect"). Unfortunately, I could not solve
this problem. However, I found that you were asked one year ago for a
similar problem in this page:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010457.html But I
must confess that I could not understand most of what was written in this
informatic experts discussion! By the way, my system is not an ubuntu, so
I think that the solution you suggested would not work in my case.

Here are the characteristics and versions of the systems installed on my
computer:
Operating system: Windows 7 professionnal, 64bits
Filezilla Client 3.7.0.1
Firefox 20.0.1

I really thank you for reading this help message and I hope that you could
explain me how to solve my problem.

I look forward to reading your answer soon,
Best regards,



--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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[galaxy-dev] liftover

[Anna Kropornicka]

Good afternoon,

I was wondering if I could get some help on the installation of the
liftover tool from UCSC. I was able to modify the liftOver.loc and
downloaded some over.chain files from UCSC to the appropriate folder. I
believe the problem extends from not having a liftover folder in my 'tools'
folder. I downloaded a local copy of galaxy called "galaxy-dist" and have
made sure it's up to date.

Thank you,

Anna Kropornicka
kroporni...@wisc.edu
Department of Genetics
University of Wisconsin-Madison

Biochemistry Addition
433 Babcock Drive, Rm 319
Madison, WI 53706

tel: (608) 262-4550x3140
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