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by Clint Winkler 06 Dec '10

06 Dec '10

Please remove me from the mailing list. Sent from my iPhone

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2011 GMOD Spring Training, March 8-12
by Dave Clements, GMOD Help Desk 03 Dec '10

03 Dec '10

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

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Merge tool and strand orientation
by Eckart Bindewald 03 Dec '10

03 Dec '10

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 -

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NGINX configuration for Galaxy production
by Richard Bruskiewich 01 Dec '10

01 Dec '10

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/nginxProxydocumentat… 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

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visualization of bed-fromat pasted text
by Sridhar A Malkaram 01 Dec '10

01 Dec '10

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

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Re: [galaxy-user] Inquiry about Cloud Computing on Galaxy
by Enis Afgan 01 Dec '10

01 Dec '10

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 > >

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MAF alignments
by pande 01 Dec '10

01 Dec '10

Hi Galaxy, Can you please enlighten me on the concept of MAF alignments ? Are they the same as BLASTZ searches ???? Thanks . Amit.

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Lift over function for ce5 (WS180) to ce6
by Zhu, Lihua (Julie) 30 Nov '10

30 Nov '10

Hi, I tried to lift over a list of chromosome mapped to WS180 (ce5) to ce6, but it seems that galaxy does not support ce5. Could you please help? Thank you very much! Best regards, Julie

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Editing a workflow - hiding intermediate datasets
by Peter 29 Nov '10

29 Nov '10

Hi all, I am quite quite puzzled about how hiding datasets is intended to work when editing a workflow. When editing a workflow, on the output of any tool (in the main part of the screen) next to the grab point for linking tools there is a "snowflake". This is either greyed out (which means hide the output when the tool is run) or yellow (which means the output is kept in the user's history), and you click on it to toggle this. Additionally, on the right hand side in the "Edit Step Actions" there can be a "Hide Dataset" action. My impression is the two UI mechanisms are intended to control the same thing - but toggling one does not affect the out (at least, not directly). For example, toggling the "snowflake" does seem to alter the right hand side (add/remove the "Hide Dataset"), but only after you save, close, and reload the workflow. Is this a bug? If so, the simplest way to solve this (from a UI perspective) might be to remove the "Hide Dataset" action from the right hand side. ------ On a related point, if I extract a workflow from my history, all the steps have their "snowflakes" greyed out - even the final step in the history. Yet despite this, when I run the new workflow all the output is kept (nothing is hidden). After a little experimenting, my guess is that you have a special case: if all the outputs have greyed out snowflakes, rather than running the tools and hidding all the output, you hide nothing. I would expect a new workflow extracted from the history to have all the output kept (yellow snowflakes), or perhaps intermediate output hidden (greyed out snowflakes) with the output from the final history step shown (yellow). Regards, Peter

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Data Library Import "tool error"
by Sridhar A Malkaram 29 Nov '10

29 Nov '10

Hi, I used the "Upload files from filesystem paths" option to upload a directory path into Galaxy Data library. I used the option NO for "Copy data into Galaxy?" as I don't want a duplicate copy of the data. I selected the hg19 for Genome. After the upload process is finished, I can see the directory tree structure, but in the "information" column for files, it reports "Job error (click name for more info)". When I click a file, for example for "macs_test_1_out.bed", which is a bed filetype, it says "failure running job tool error" under "Miscellaneous information". I am pasting below the whlole information. This happens for all the data files that are uploaded. What is this error? and which tool it is complaining about? My another question is, can we upload files/directories with compressed format files (.tar, .gz, .bz. etc) and binary files like .doc, .xls ? If so, what additional plugins we need to have in place? Thanks in advance for your suggestions. ================================ Message: Galaxy Test-data Uploaded by: Date uploaded: 2010-11-29 File size: 52.2 Kb Data type: data Build: hg19 Miscellaneous information: failure running job tool error Database/Build: hg19 Peek: Disk file: /mnt/bioinfo/LINKS/Biotin/data/work/galaxy-dist/test-data/peakcalling_macs/macs_test_1_out.bed ================================ -- With Regards, Sridhar Postdoctoral Research Associate Nutrition and Health Sciences University of Nebraska-Lincoln

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