miRNA targets at all transcribed but not translated sites at genome level
by Abhay Krishna
I have an intuitive feeling, It will be possible to do it in Galaxy,
to be precise:
I want to find all miRNA targets at whole genome level (These targets should
be transcribed but not translated), in other words pseudogenes and other non
coding rna.
Any ideas? How to get this.
Best
Abhay
10 years, 12 months
Unsubscribe
by Clint Winkler
Please remove me from the mailing list.
Sent from my iPhone
10 years, 12 months
2011 GMOD Spring Training, March 8-12
by Dave Clements, GMOD Help Desk
Applications are now being accepted for the 2011 GMOD Spring Training
course a five-day hands-on school aimed at teaching new GMOD
administrators how to install, configure and integrate popular GMOD
components. The course will be held March 8-12 at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as
part of GMOD Americas 2011.
Links:
* http://gmod.org/wiki/2011_GMOD_Spring_Training
* http://gmod.org/wiki/GMOD_Americas_2011
* http://www.nescent.org/
These components will be covered:
* Apollo - genome annotation editor
* Chado - biological database schema
* Galaxy - workflow system
* GBrowse - genome viewer
* GBrowse_syn - synteny viewer
* GFF3 - genome annotation file format and tools
* InterMine - biological data mining system
* JBrowse - next generation genome browser
* MAKER - genome annotation pipeline
* Tripal - web front end to Chado databases
The deadline for applying is the end of Friday, January 7, 2011.
Admission is competitive and is based on the strength of the
application, especially the statement of interest. The 2010 school had
over 60 applicants for the 25 slots. Any application received after
deadline will be automatically placed on the waiting list.
The course requires some knowledge of Linux as a prerequisite. The
registration fee will be $265 (only $53 per day!). There will be a
limited number of scholarships available.
This may be the only GMOD School offered in 2011. If you are
interested, you are strongly encouraged to apply by January 7.
Thanks,
Dave Clements
--
http://gmod.org/wiki/GMOD_Americas_2011
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Help_Desk_Feedback
11 years
Merge tool and strand orientation
by Eckart Bindewald
Hello:
let me start by saying that I am very impressed by the service the
Galaxy web server provides to the community; it has proven very useful
for my work.
Today I came across a situation that puzzles me. I am trying to merge
exons corresponding to the same gene (but possibly from different
splice variants).
At the bottom of this email I am listing, as an example, the 153 exons
that are related to the different splice variants of FlyBase gene
CG32491 (obtained by the pattern matching (tool "Select lines that
match an expression" and pattern .+CG32491-. ) applied to the data
set of FlyBaseGene exons (110,472 exons, genome assembly dm3). I am
using bed format and the general Galaxy web server.
If I now apply the "Merge" tool to the intervals, I obtain 26
intervals (listed further below). Now applying the "subtract" tool to
the original 153 exons results in 8 "leftover" regions that I did not
expect. Somehow they seem to be missing in the merge result.
I then deactivated the strand information in the interval set of 153
exons. Applying the merge tool now results in 34 intervals (again
listed below). Checking the result via the subtract tool (subtracting
the merge result from the original data set of 153 exons) results, as
expected, in zero intervals.
So my questions are:
- is this the intended functionality of the tools? Maybe one can add
statements regarding these issues in the tool documentation.
- why does the outcome of the merge operation depend on whether the
"strand" column is set or not? The original set of intervals all had
the same negative strand orientation, so it appears to me that the
merge operation should give the same result in both cases.
- subtracting the merged intervals (that do not have strand
information) from the set of 153 intervals results in 8 strands that
now have positive strand orientation (they originally had negative
strand orientation). Why does subtracting a set of intervals without
strand information from a set of intervals with strand information
change the strand orientation of the first set?
Any comments are highly appreciated!
Thanks,
Eckart
Dr. Eckart Bindewald (Contractor)
SAIC-Frederick, Inc.
Center for Cancer Research Nanobiology Program
National Cancer Institute
P.O. Box B
Frederick, MD 21702 USA
Phone: 301-846-5538
Fax: 301-846-5598
E-mail: eckart(a)mail.nih.gov
Here is the result (34 regions) of the merge operation (not using
strand orientation) applied to the 153 exon regions listed further
below ;
chr3R 17177330 17177608
chr3R 17177760 17178959
chr3R 17179070 17179456
chr3R 17179617 17180053
chr3R 17180159 17180416
chr3R 17180695 17181279
chr3R 17181479 17181973
chr3R 17182071 17182426
chr3R 17182532 17182690
chr3R 17182776 17183086
chr3R 17183242 17183480
chr3R 17183726 17183926
chr3R 17184011 17184791
chr3R 17186111 17186276
chr3R 17186349 17187009
chr3R 17187119 17187332
chr3R 17187391 17187860
chr3R 17187909 17188590
chr3R 17188688 17189606
chr3R 17189739 17190097
chr3R 17190173 17190367
chr3R 17190435 17190714
chr3R 17191725 17192060
chr3R 17192171 17192466
chr3R 17193631 17193960
chr3R 17194101 17194784
chr3R 17195183 17196364
chr3R 17196654 17196949
chr3R 17197044 17197789
chr3R 17197884 17198802
chr3R 17200781 17201634
chr3R 17202323 17202463
chr3R 17202540 17202798
chr3R 17203009 17203121
Here is the result (26 regions) of the merge operation (using strand
orientation) applied to the 153 exon regions listed further below ;
chr3R 17177330 17177608
chr3R 17177760 17178959
chr3R 17179070 17179456
chr3R 17179617 17180053
chr3R 17180159 17180416
chr3R 17180695 17181279
chr3R 17181479 17181973
chr3R 17182071 17182426
chr3R 17182532 17182690
chr3R 17182776 17183086
chr3R 17183242 17183480
chr3R 17183726 17183926
chr3R 17184011 17184791
chr3R 17187909 17188590
chr3R 17188688 17189606
chr3R 17189739 17190097
chr3R 17190173 17190367
chr3R 17190435 17190714
chr3R 17195821 17196364
chr3R 17196654 17196949
chr3R 17197044 17197789
chr3R 17197884 17198802
chr3R 17200781 17201634
chr3R 17202323 17202463
chr3R 17202540 17202798
chr3R 17203009 17203121
Here are the 8 "leftover" regions from the original 153 exons that do
not intersect with the result of the 26 merged regions (result of
subtract tool of 153 exons that do not overlap with 26 merged exons;
note the change strand orientation):
chr3R 17186111 17186276 CG32491-RT_exon_0_0_chr3R_17186112_f 0 +
chr3R 17186349 17187009 CG32491-RT_exon_1_0_chr3R_17186350_f 0 +
chr3R 17187119 17187332 CG32491-RZ_exon_0_0_chr3R_17187120_f 0 +
chr3R 17187391 17187860 CG32491-RZ_exon_1_0_chr3R_17187392_f 0 +
chr3R 17191725 17192060 CG32491-RY_exon_0_0_chr3R_17191726_f 0 +
chr3R 17192171 17192466 CG32491-RX_exon_0_0_chr3R_17192172_f 0 +
chr3R 17193631 17193960 CG32491-RW_exon_0_0_chr3R_17193632_f 0 +
chr3R 17194101 17194784 CG32491-RV_exon_0_0_chr3R_17194102_f 0 +
Here are the 153 exons related to FlyBase gene CG32491 obtained by the
pattern matching (tool "Select lines that match an expression" and
pattern .+CG32491-. ) applied to the data set of FlyBaseGene exons
(110,472 exons):
chr3R 17177330 17177608 CG32491-RR_exon_0_0_chr3R_17177331_r 0 -
chr3R 17200781 17201634 CG32491-RR_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RR_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RR_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RR_exon_4_0_chr3R_17203010_r 0 -
chr3R 17177760 17178358 CG32491-RA_exon_0_0_chr3R_17177761_r 0 -
chr3R 17200781 17201634 CG32491-RA_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RA_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RA_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RA_exon_4_0_chr3R_17203010_r 0 -
chr3R 17178092 17178959 CG32491-RF_exon_0_0_chr3R_17178093_r 0 -
chr3R 17200781 17201634 CG32491-RF_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RF_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RF_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RF_exon_4_0_chr3R_17203010_r 0 -
chr3R 17179070 17179456 CG32491-RD_exon_0_0_chr3R_17179071_r 0 -
chr3R 17200781 17201634 CG32491-RD_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RD_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RD_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RD_exon_4_0_chr3R_17203010_r 0 -
chr3R 17179617 17180053 CG32491-RAC_exon_0_0_chr3R_17179618_r 0 -
chr3R 17200781 17201634 CG32491-RAC_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RAC_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RAC_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RAC_exon_4_0_chr3R_17203010_r 0 -
chr3R 17180159 17180416 CG32491-RG_exon_0_0_chr3R_17180160_r 0 -
chr3R 17180695 17180811 CG32491-RG_exon_1_0_chr3R_17180696_r 0 -
chr3R 17200781 17201634 CG32491-RG_exon_2_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RG_exon_3_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RG_exon_4_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RG_exon_5_0_chr3R_17203010_r 0 -
chr3R 17180159 17180416 CG32491-RH_exon_0_0_chr3R_17180160_r 0 -
chr3R 17180695 17181279 CG32491-RH_exon_1_0_chr3R_17180696_r 0 -
chr3R 17200781 17201634 CG32491-RH_exon_2_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RH_exon_3_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RH_exon_4_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RH_exon_5_0_chr3R_17203010_r 0 -
chr3R 17180159 17180416 CG32491-RQ_exon_0_0_chr3R_17180160_r 0 -
chr3R 17200781 17201634 CG32491-RQ_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RQ_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RQ_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RQ_exon_4_0_chr3R_17203010_r 0 -
chr3R 17180941 17181279 CG32491-RB_exon_0_0_chr3R_17180942_r 0 -
chr3R 17181479 17181973 CG32491-RB_exon_1_0_chr3R_17181480_r 0 -
chr3R 17200781 17201634 CG32491-RB_exon_2_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RB_exon_3_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RB_exon_4_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RB_exon_5_0_chr3R_17203010_r 0 -
chr3R 17182071 17182426 CG32491-RI_exon_0_0_chr3R_17182072_r 0 -
chr3R 17182532 17182690 CG32491-RI_exon_1_0_chr3R_17182533_r 0 -
chr3R 17200781 17201634 CG32491-RI_exon_2_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RI_exon_3_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RI_exon_4_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RI_exon_5_0_chr3R_17203010_r 0 -
chr3R 17182776 17183086 CG32491-RJ_exon_0_0_chr3R_17182777_r 0 -
chr3R 17200781 17201634 CG32491-RJ_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RJ_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RJ_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RJ_exon_4_0_chr3R_17203010_r 0 -
chr3R 17183242 17183480 CG32491-RP_exon_0_0_chr3R_17183243_r 0 -
chr3R 17183726 17183926 CG32491-RP_exon_1_0_chr3R_17183727_r 0 -
chr3R 17200781 17201634 CG32491-RP_exon_2_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RP_exon_3_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RP_exon_4_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RP_exon_5_0_chr3R_17203010_r 0 -
chr3R 17184011 17184791 CG32491-RK_exon_0_0_chr3R_17184012_r 0 -
chr3R 17200781 17201634 CG32491-RK_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RK_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RK_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RK_exon_4_0_chr3R_17203010_r 0 -
chr3R 17184021 17184318 CG32491-RL_exon_0_0_chr3R_17184022_r 0 -
chr3R 17200781 17201634 CG32491-RL_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RL_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RL_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RL_exon_4_0_chr3R_17203010_r 0 -
chr3R 17186111 17186276 CG32491-RT_exon_0_0_chr3R_17186112_f 0 .
chr3R 17186349 17187009 CG32491-RT_exon_1_0_chr3R_17186350_f 0 .
chr3R 17200781 17201634 CG32491-RT_exon_2_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RT_exon_3_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RT_exon_4_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RT_exon_5_0_chr3R_17203010_f 0 .
chr3R 17187119 17187332 CG32491-RZ_exon_0_0_chr3R_17187120_f 0 .
chr3R 17187391 17187860 CG32491-RZ_exon_1_0_chr3R_17187392_f 0 .
chr3R 17200781 17201634 CG32491-RZ_exon_2_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RZ_exon_3_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RZ_exon_4_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RZ_exon_5_0_chr3R_17203010_f 0 .
chr3R 17187909 17188590 CG32491-RM_exon_0_0_chr3R_17187910_r 0 -
chr3R 17200781 17201634 CG32491-RM_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RM_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RM_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RM_exon_4_0_chr3R_17203010_r 0 -
chr3R 17188688 17189606 CG32491-RE_exon_0_0_chr3R_17188689_r 0 -
chr3R 17200781 17201634 CG32491-RE_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RE_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RE_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RE_exon_4_0_chr3R_17203010_r 0 -
chr3R 17189739 17190097 CG32491-RAB_exon_0_0_chr3R_17189740_r 0 -
chr3R 17200781 17201634 CG32491-RAB_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RAB_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RAB_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RAB_exon_4_0_chr3R_17203010_r 0 -
chr3R 17190173 17190367 CG32491-RC_exon_0_0_chr3R_17190174_r 0 -
chr3R 17190435 17190714 CG32491-RC_exon_1_0_chr3R_17190436_r 0 -
chr3R 17200781 17201634 CG32491-RC_exon_2_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RC_exon_3_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RC_exon_4_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RC_exon_5_0_chr3R_17203010_r 0 -
chr3R 17191725 17192060 CG32491-RY_exon_0_0_chr3R_17191726_f 0 .
chr3R 17200781 17201634 CG32491-RY_exon_1_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RY_exon_2_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RY_exon_3_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RY_exon_4_0_chr3R_17203010_f 0 .
chr3R 17192171 17192466 CG32491-RX_exon_0_0_chr3R_17192172_f 0 .
chr3R 17200781 17201634 CG32491-RX_exon_1_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RX_exon_2_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RX_exon_3_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RX_exon_4_0_chr3R_17203010_f 0 .
chr3R 17193631 17193960 CG32491-RW_exon_0_0_chr3R_17193632_f 0 .
chr3R 17200781 17201634 CG32491-RW_exon_1_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RW_exon_2_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RW_exon_3_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RW_exon_4_0_chr3R_17203010_f 0 .
chr3R 17194101 17194784 CG32491-RV_exon_0_0_chr3R_17194102_f 0 .
chr3R 17200781 17201634 CG32491-RV_exon_1_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RV_exon_2_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RV_exon_3_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RV_exon_4_0_chr3R_17203010_f 0 .
chr3R 17195183 17195967 CG32491-RU_exon_0_0_chr3R_17195184_f 0 .
chr3R 17200781 17201634 CG32491-RU_exon_1_0_chr3R_17200782_f 0 .
chr3R 17202323 17202463 CG32491-RU_exon_2_0_chr3R_17202324_f 0 .
chr3R 17202540 17202798 CG32491-RU_exon_3_0_chr3R_17202541_f 0 .
chr3R 17203009 17203121 CG32491-RU_exon_4_0_chr3R_17203010_f 0 .
chr3R 17195821 17196364 CG32491-RS_exon_0_0_chr3R_17195822_r 0 -
chr3R 17200781 17201634 CG32491-RS_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RS_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RS_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RS_exon_4_0_chr3R_17203010_r 0 -
chr3R 17196654 17196949 CG32491-RAA_exon_0_0_chr3R_17196655_r 0 -
chr3R 17200781 17201634 CG32491-RAA_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RAA_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RAA_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RAA_exon_4_0_chr3R_17203010_r 0 -
chr3R 17197044 17197789 CG32491-RO_exon_0_0_chr3R_17197045_r 0 -
chr3R 17200781 17201634 CG32491-RO_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RO_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RO_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RO_exon_4_0_chr3R_17203010_r 0 -
chr3R 17197884 17198802 CG32491-RN_exon_0_0_chr3R_17197885_r 0 -
chr3R 17200781 17201634 CG32491-RN_exon_1_0_chr3R_17200782_r 0 -
chr3R 17202323 17202463 CG32491-RN_exon_2_0_chr3R_17202324_r 0 -
chr3R 17202540 17202798 CG32491-RN_exon_3_0_chr3R_17202541_r 0 -
chr3R 17203009 17203121 CG32491-RN_exon_4_0_chr3R_17203010_r 0 -
11 years
NGINX configuration for Galaxy production
by Richard Bruskiewich
Colleagues,
I encountered a curious problem while configuring nginx as a proxy for
Galaxy. I posed the question through Enis who forwarded it to one of the
lists. I just want to share a solution to the issue, which could perhaps be
documented in a small change to the
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxydocument...
page.
The observed problem was that Galaxy proxied through NGINX would only
display properly in Microsoft IE but not in Firefox or Opera. One of my
colleagues noticed that a Firefox error console reported that the various
cascading style sheets were observed as having MIME type "text/plain" not
"text/css" hence, where not loaded by Firefox. Presumably IE assumed CSS
file type by the context of retrieval but the other browsers were more
strict.
Anyhow, this suggested that although NGINX has a configuration file of MIME
types associated with file extensions, the content-type wasn't being
properly set. I don't know if this represents a bug in NGINX operations, but
after perusing the NGINX wiki docs, I came across a directive that appeared
to solve the problem: default_type.
The "default_type" covers any files in a specified context (http, server,
location) which don't otherwise have their MIME type recognized (for
whatever reason) and is itself originally set "by default" to "text/plain",
which may explain the observed error in content type sent back.
What I therefore did is reset the default type, in the style sheet nginx
"location" directive context, to "text/css". This appeared to work.
In the nginxProxy wiki documentation page on BitBucket, somebody with
editorial privileges to this page may wish to document this throughout the
page where the style directives are documented , i.e.
location /static/style {
alias /home/nate/galaxy_dist/static/june_2007_style/blue;
default_type text/css;
# other directives...
}
Cheers,
Richard Bruskiewich, PhD
Senior Scientist, Computational and Systems Biology
Applications Team for Computational Genomics
T.T. Chang Genetic Resources Center
International Rice Research Institute
11 years
visualization of bed-fromat pasted text
by Sridhar A Malkaram
Hi,
When loading pasted text with lines in bed format (chrom, start,
end), I find that galaxy can't display it in the visualization.
Does the visualization need specific bed format , with all the
columns (~13)? Are gff format/Sam format files supported?
With Regards,
Sridhar
Postdoctoral Research Associate
Nutrition and Health Sciences
University of Nebraska-Lincoln
11 years
Re: [galaxy-user] Inquiry about Cloud Computing on Galaxy
by Enis Afgan
Hi,
Unfortunately Galaxy does not have a ready option to be used on a Hadoop
based cluster. I am not familiar with methods of interacting with hadoop
clusters; however, if there is DRMAA support for a hadoop manager, the
interaction should be fairly straightforward. The distribution of job load
however, may be more involved.
I'm cc-ing the galaxy-user list so this question gets more attention and
possibly a more complete answer.
Enis
On Wed, Dec 1, 2010 at 4:07 PM, Xiandong Meng <xiandongmeng(a)lbl.gov> wrote:
> Hi Enis,
> Thank you for your great work on Galaxy Cloud. I am running a galaxy
> server for sequence analysis at Berkeley Lab. The galaxy works wel with
> our SGE clusters l. Due to the size of data, I am going to move the
> computation to a cloud computing using a Hadoop cluster. So far I only found
> information about cloud solution on Amazon EC2. I was wondering if Galaxy
> has a mechanism to support a general Hadoop cluster just like running a SGE
> or PBS cluster.
>
> I would greatly apprecuiate if you give me some hints.
>
> Thanks&Regards,
> X. Meng
>
>
11 years
MAF alignments
by pande
Hi Galaxy,
Can you please enlighten me on the concept of MAF
alignments ? Are they the same as BLASTZ searches ????
Thanks .
Amit.
11 years
