Installing galaxy with Apache ...
by Neil.Burdett＠csiro.au
Hi
I've installed galaxy with the default settings and it works fine.
On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation.
After installing Apache I can put my ip address into a browser and I get message saying Apache is working fine. It displays a message from /var/www/index.html
Now when I start galaxy I was assuming I would get redirected to the galaxy welcome page, but this doesn't happen and it remains at /var/www/index.html. To view the welcome page I have to add ":8080" after the ip address. Is this still required? I thought that Apache would know to redirect to my distribution....What am I doing wrong?
/etc/apache2/sites-available/default-ssl and /etc/apache2/sites-available/default look like this ...
DocumentRoot /var/www
<Directory />
Options FollowSymLinks
AllowOverride None
</Directory>
<Directory /var/www/>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
etc ...
/var/www/.htaccess
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
I created an empty 'galaxy' directory with 777 permissions on it under /var/www
and universe_wsgi.ini
# Define the proxy-prefix filter.
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
# ---- Galaxy ---------------------------------------------------------------
# Configuration of the Galaxy application.
[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy
Thanks Neil
10 years, 3 months
How to decide if the deference is significant
by Du, Jianguang
Dear All,
I am looking for the deferential splicing events between cell types. I have run the Cuffdiff and I am going through the output file "splicing differential expression testing". I have read the documentation and protocols about how Cuffdiff test for differential expression and regulation. However although I know the changes in relative abundance are quantified by the square root of the Jensen-Shannon divergence, I still could not understand the concept of it (unfortunately I am not good at math and statistics). Is there any way to convert "the square root of the Jensen-Shannon divergence" into "fold of diference"? How much of "the square root of the Jensen-Shannon divergence" equals to 2 fold of difference?
Thanks.
Jianguang
10 years, 3 months
Is there web-based CummeRbund?
by Du, Jianguang
Dear All,
I am going to visualize Cuffdiff outputs. I understand that CummeRbund can be used to visualize Cuffdiff outputs. However, I am not good at Linux system and feel difficult to understand CummeRbund manual. Is there web-based CummeRbund program (like Tophat and Cufflink) available for use?
If web-based CummeRbund does not exist, is there other web-based program can be used to visualize Cuffdiff outputs?
Thanks.
Jianguang
10 years, 3 months
Text Manipulation
by Jennifer Jackson
Post to mailing list
On 8/26/12 11:38 AM, LeeMSilver(a)genepeeks.com wrote:
> Hi Jen,
>
> The ability to use Python commands with the Compute tool seems to be a very well-hidden gem in Galaxy. The problem with this nearly unmentioned gem is the sheer frustration felt when something that works on the Python command line fails on the Galaxy Compute tool.
>
> What I would like to do is manipulate a column from a UCSC download that lists two or three codons separated by a comma, e.g. AAC,GCG, or GGT, CAC, TAT, . The string-based split command < c5.split(",").pop(1) > fails on this data because Galaxy assigned it a <list> type automatically. All of my attempts to change the data type to "string" have failed.
>
> Any suggestions?
>
> Lee
> LeeMSilver(a)genepeeks.com
--
Jennifer Jackson
http://galaxyproject.org
10 years, 3 months
Please help with the settings for Cufflink, Cuffmerge and Cuffdiff
by Du, Jianguang
Dear All,
I am looking for the differential splicing events between cell types.
Although I got a lot of helps from Jen and from protocols found online, I am still not sure about some settings for Cufflink, Cuffmerge and Cuffdiff.
1) For Cufflink:
There is a setting for Bias Correction. I made the setting as below:
Perform Bias Correction: Yes
Reference sequence data: Locally cached
Did I make the right settings?
2) For Cuffmerge:
As for whether use sequence data, I made the setting as below:
Use Sequence Data: Yes
Choose the source for the reference list: Locally cached
Did I make the right settings?
3) For Cuffdiff:
There is another choice whether perform Bias Correction, I made the setting as below:
Perform Bias Correction: Yes
Reference sequence data: Locally cached
Did I make the right settings?
Thanks.
Jianguang
10 years, 3 months
Galaxy-France -- Communauté française de Galaxy (French Galaxy Community)
by Dave Clements
Bonjour à tous,
Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en
ligne la liste de diffusion Galaxy France.
Cette liste a pour but de partager et communiquer sur nos différentes
expériences avec Galaxy au sein de l'hexagone.
La langue officielle de cette liste est le français.
Vous avez besoin d'aide dans l'utilisation de Galaxy,
Vous hébergez un serveur public Galaxy,
Vous maintenez une instance locale de Galaxy,
Vous venez de déposer un outil sur le toolshed,
Vous avez des trucs et astuces pouvant interresser la communauté,
Vous organisez des formations avec Galaxy,
Rejoignez nous en vous inscrivant à
http://lists.bx.psu.edu/listinfo/galaxy-france
Les archives de cette liste sont disponibles à
http://france.list.galaxyproject.org
A très bientôt sur la liste Galaxy France,
Les administrateurs:
Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer
Jackson
------------------------------
---------------------
Hi everyone,
With the help and the support of the Galaxy team, we just put online the
Galaxy French mailing list.
The aim of this list is to share and communicate on our different
experiences with Galaxy in France.
* The main language is French.
*
Topics include, but are not limited to:
You need help in the use of Galaxy,
You're hosting a Galaxy public server,
You're maintaining a local instance of Galaxy,
You just add a new tool on the toolshed,
You have some tips that could interested the community,
You organize workshops with Galaxy,
Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france
The list's archives are also available at
http://france.list.galaxyproject.org
See you soon on the Galaxy-France list,
The administrators:
Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer
Jackson
--
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
10 years, 3 months
Please help me check the quality of the Tophat mapping to reference genome
by Du, Jianguang
Dear All,
I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat output (the file of accepted hits). I got the diagnosis results as follow:
9471730 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
9471730 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
I ran Tophat with settings as shown below:
Will you select a reference genome from your history or use a built-in index?
Use a built-in index
Select a reference genome
/galaxy/data/mm9/bowtie_index/mm9
Is this library mate-paired?
Single-end
TopHat settings to use
Full parameter list
Library Type
FR Unstranded
Anchor length (at least 3)
8
Maximum number of mismatches that can appear in the anchor region of spliced alignment
0
The minimum intron length
70
The maximum intron length
500000
Allow indel search
Yes
Max insertion length.
3
Max deletion length.
3
Maximum number of alignments to be allowed
20
Minimum intron length that may be found during split-segment (default) search
50
Maximum intron length that may be found during split-segment (default) search
500000
Number of mismatches allowed in the initial read mapping
1
Number of mismatches allowed in each segment alignment for reads mapped independently
1
Minimum length of read segments
25
Use Own Junctions
Yes
Use Gene Annotation Model
Yes
Gene Model Annotations
iGenome version of mm9 genes. GTF
Use Raw Junctions
No
Only look for supplied junctions
No
Use Closure Search
No
Use Coverage Search
Yes
Minimum intron length that may be found during coverage search
50
Maximum intron length that may be found during coverage search
20000
Use Microexon Search
No
Please help me find out what is wrong with the Tophat.
Thanks,
Jianguang
10 years, 3 months
Calling SNP
by Francesco Vitiello
Hi everyone,
I'ha a dataset from a sample in Illumina format. I've already groomed the
file and aligned to hg19. How can I call SNPs and remove the most common
and generally not dangerous?
Thank a lot.
Francesco
--
--
10 years, 3 months
Extract Spliced Transcripts from Cuffmerge
by Hanson, Sara J
Hi All,
I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them into transcripts using the Tuxedo pipeline. II have used the "Extract Genomic DNA" tool to pull the annotated genes out of the genome assembly, but I would like the spliced transcripts as well. Is there a tool or pipeline that can retrieve the exons individually and concatenate them if they are part of the same gene? Any help on this would be much appreciated.
Thanks!
10 years, 3 months
Is tss_id unique for each transcript?
by Du, Jianguang
Dear All,
I am reading and comparing the outputs of Cuffdiff. I found there is a "tss_id" column in "transcript FPKM tracking", "gene FPKM tracking", "TSS groups FPKM tracking" and "CDS FPKM tracking" files. In this column, each line has a unique label such as "TSS1001". This kind of labels also appear under "test_id" column in "TSS groups differential expression testing" and "splicing defferential expression testing" files. Does each of this kind label represent a unique transcript? In other word, does each transcript has a unique label initiating with TSS followed by numbers?
Thank.
Jianguang
10 years, 3 months
