[galaxy-dev] Plot-bamstats

[Jose Juan Almagro Armenteros]

Hello,

I have just installed the tool "samtools_stats" from the toolshed. In the
synopsis says: "This tool runs the samtools stats command in the SAMtools
toolkit, collecting statistics from BAM files. The output can be visualized
using plot-bamstat ", but I haven't found any tool to visualize it with
plot-bamstat.

Do you know if there is such tool or another similar?

Best regards,

Jose
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[galaxy-dev] Fwd: Seeking Help with Galaxy

[Anton Nekrutenko]

Tendai:

I'm forwarding your e-mail to the dev forum. This is the best place to ask
these kinds of questions.

a.


-- Forwarded message --
From: Mutangadura, Tendai 
Date: Thu, Oct 15, 2015 at 7:17 PM
Subject: Seeking Help with Galaxy
To: "an...@bx.psu.edu" 
Cc: "Mutangadura, Tendai" 


Dr. Nekrutenko,

I have been trying to learn how to use Galaxy using the Galaxy Main Server
for some time but I have just convinced my boss to allow me to convert a
computer that was laying idle as a Linux machine and I am planning to
install my local instance of Galaxy there. I have been watching some of
your Vimeo instructional videos on using Galaxy and I wanted to find out if
I could from time to ask you or your mentees questions as I try to set up
my Galaxy instance.

My first question is this: is there a difference between downloading and
installing tools to the cloud and doing the same installation on my Linux
desktop? (I downloaded 2 of your videos yesterday on doing this on the
cloud).

My Linux computer has Centos7 installed on it, has 500GB storage and 8GB
RAM. I also have 5 a TB external hard drive that I can use in conjunction
with the desktop. Can I accomplish much more with this compared to what I
can do on my main server Galaxy account?

The main focus of our lab is the use of whole genome sequencing (WGS) to
discover disease causing mutations in dogs, and our lab has made several
discoveries this way. Like many reference genomes, the dog genome reference
has quite a few gaps. My immediate aim after installing my local instance
of Galaxy is to use a 88200 bp bac sequence that bridges a gap in the dog
reference that our collaborators made available to us (they filled the gap
by Sanger Sequencing/chromosome walking) and use this as the reference
sequence to align against reads from various dogs that we have whole genome
sequences for. If you have the time, could you please give me some guidance
as to the best way to do this?

The bac sequence is already in fasta format. I have access to WGS files of
raw sequence reads in the original, unprocessed state as in the form in
which the reads came off the Illumina sequencing machine, and also in
versions subsequent to our bionformatician’s quality control manipulation
and error correction (using MaSuRCA.  My plan is to start practicing
(before my local Galaxy is up and running) by

1.   Uploading the bac sequence and use this as my ‘reference”

2.   Upload all the paired reads for one dog

3.   Align the paired reads using appropriate software (BWA?)

4.   Call Variants using Freebayes?

5.   Do this for several dogs and compare the VCF of the various dogs

6.   Hope to identify disease-causing variants that we potentially
missed due to no alignment because the reads have no sequence to align to.

7.   After this I hope to come up with a workflow which I can save and
export to my local Galaxy.

(I already have the above sequences uploaded into my Galaxy main server
account).

Thank you for your time and for posting the instructional videos that I
have already learnt so much from.

Tendai Mutangadura

(I publish papers as Tendai Mhlanga-Mutangadura)





-- 
Anton Nekrutenko
Professor of Biochemistry
and Molecular Biology
*http://nekrut.bx.psu.edu *
(814) 826-3051
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Re: [galaxy-dev] CloudMan launch error

[Aaron Darling]

Thanks for the reply Enis,

I had some off-list discussion with Simon Gladman about this. Simon
indicated it seems that OpenStack security groups are not propagating to
worker nodes at startup. Manually configuring the worker node security
group and then rebooting the master appears to be a workaround.
Hopefully this is only a temporary issue, and obviously one that's
specific to NeCTAR.

Cheers,
-Aaron

On Thu, 2015-10-15 at 21:59 -0400, Enis Afgan wrote:
> Hi Aaron,
> 
> Does the "AMQP Connection Failure:" error continue indefinitely?
> It would be helpful to see the log files from the time a worker is
> being added as well as the CloudMan logs from a worker node. It
> appears you're launching GVL v3.04 however, the default is now 4.0.0.
> Have you tried keeping the defaults?
> 
> 
> 
> 
> PS
> I'm cc'ing h...@genome.edu.au as the default help mailing list for the
> GVL.
> 
> 
> On Wed, Oct 14, 2015 at 11:31 PM, Aaron Darling
>  wrote:
> 
> Hi all, I'm new to CloudMan, and trying to launch a cluster
> via GVL (3 or 4) on NeCTAR.
> I'm able to get a head node running without trouble via
> launch.genome.edu.au, but launching worker nodes from the
> CloudMan interface appears to fail. CloudMan reboots the
> worker repeatedly before giving up. I logged into the worker
> to inspect log files and found the following, but it's not
> obvious to me what to do next. Hope this is something simple?
> 
> 
> ubuntu@server-fbbd9a10-fb58-48d8-89cd-5ddd22821648:~$
> cat /mnt/cm/paster.log
> Python version:  (2, 7)
> Image configuration suports: {'apps': ['cloudman', 'galaxy']}
> 2015-10-15 14:15:24,973 DEBUGapp:73   Initializing
> app
> 2015-10-15 14:15:24,973 DEBUGec2:109  Gathering
> instance zone, attempt 0
> 2015-10-15 14:15:25,140 DEBUGec2:115  Instance
> zone is 'NCI'
> 2015-10-15 14:15:25,140 DEBUGec2:44   Gathering
> instance ami, attempt 0
> 2015-10-15 14:15:25,459 DEBUGapp:76   Running on
> 'openstack' type of cloud in zone 'NCI' using image
> 'ami-3484'.
> 2015-10-15 14:15:25,459 DEBUGapp:98   Getting
> pd.yaml
> 2015-10-15 14:15:25,459 DEBUG  openstack:99   Establishing
> a boto Swift connection.
> 2015-10-15 14:15:25,459 DEBUG  openstack:109  Got boto
> Swift connection.
> 2015-10-15 14:15:26,112 DEBUG   misc:578  Retrieved
> file 'persistent_data.yaml' from bucket
> 'cm-45b53bf5024e962bd27e15fd81fcc07d' on host
> 'swift.rc.nectar.org.au' to 'pd.yaml'.
> 2015-10-15 14:15:26,118 INFO app:119  Worker
> starting
> 2015-10-15 14:15:26,136 DEBUGec2:76   Gathering
> instance id, attempt 0
> 2015-10-15 14:15:26,338 DEBUGec2:82   Instance ID
> is 'i-0019a2fc'
> 2015-10-15 14:16:29,488 DEBUG   comm:134  AMQP
> Connection Failure:  [Errno 110] Connection timed out
> 2015-10-15 14:16:29,492 DEBUG   base:57   Enabling
> 'root' controller, class: CM
> 2015-10-15 14:16:29,494 DEBUG   buildapp:93   Enabling
> 'httpexceptions' middleware
> 2015-10-15 14:16:29,496 DEBUG   buildapp:99   Enabling
> 'recursive' middleware
> 2015-10-15 14:16:29,499 DEBUG   buildapp:119  Enabling
> 'print debug' middleware
> 2015-10-15 14:16:29,506 DEBUG   buildapp:133  Enabling
> 'error' middleware
> 2015-10-15 14:16:29,507 DEBUG   buildapp:143  Enabling
> 'config' middleware
> 2015-10-15 14:16:29,508 DEBUG   buildapp:147  Enabling
> 'x-forwarded-host' middleware
> 2015-10-15 14:16:29,517 DEBUG   misc:768
> 'cp /etc/hosts /etc/hosts.orig' command OK
> 2015-10-15 14:16:29,528 DEBUG   misc:768
> 'cp /tmp/tmpuV3NTJ /etc/hosts' command OK
> Starting server in PID 2825.
> 2015-10-15 14:16:29,533 DEBUG   misc:768  'chmod
> 644 /etc/hosts' command OK
> 2015-10-15 14:16:29,533 DEBUG worker:558  Trying to
> setup AMQP connection; conn = ' object at 0x2743950>'
> serving on 0.0.0.0:42284 view at http://127.0.0.1:42284
> 2015-10-15 14:17:32,656 DEBUG   comm:134  AMQP
> Connection Failure:  [Errno 110] Connection timed out
> 2015-10-15 14:17:32,656 DEBUG worker:558  Trying to
> setup AMQP connection; conn = ' object at 0x2743950>'
> 2015-10-15 14:18:35,760 DEBUG   comm:134  AMQP
> Connection Failure:  [Errno 110] Connection timed out
> 2015-10-15 14:18:35,760 DEBUG worker:558  Trying to
> setup AMQP