Re: [galaxy-user] visualization through Trackster on local Galaxy installation
Using full path in the ini file fix the problem! Thanks, Yupu On Jan 30, 2014, at 10:21, Jennifer Jackson j...@bx.psu.edu wrote: Hi Yupu, I'm sorry, I mixed up the processing for custom builds with the processing for installed builds in my initial reply. A .2bit .len file are appropriate for what you are doing - and the wiki instructions are accurate. Still, I double checked with Jeremy, the scientist that developed the tool, about your issue. He found that the full path to the .len file needs to be specified right now in order for installed builds to function correctly. This deviates from the wiki instructions, but we consider this a bug and plan to correct it in the next release. Please try using the full path and let us know how that works out, Jen Galaxy team On 1/29/14 11:54 AM, Yupu Liang wrote: Dear Jennifer: Hi, I did put 2bit file as suggested by https://wiki.galaxyproject.org/Visualization%20Setup. Should I get rid of the len file? and I assume I will also need to take off the len_file_path out of the universe_wsgi.ini file. In term of using .fasta file. I have them and I am not clear where I should put them for visualization purpose and also what adjustment i need to make in the ini file. Any help would be appreciated and I am really excited about doing all the visualization within Galaxy. I think the biologists would really love these features. Thanks a lot, Yupu On Jan 29, 2014, at 14:21, Jennifer Jackson j...@bx.psu.edu wrote: Hello Yupu, Using a .len file is problematic at this time. In the upcoming release this will be corrected. Using a .fasta file is the solution. In many cases, using a .fasta file can be preferred as it will include the reference genome sequence in the visualization, but the choice is yours, once the correction is released to the distribution. More about this is in a recent post from Jeremy: http://lists.bx.psu.edu/pipermail/galaxy-user/2014-January/007106.html Our apologies for the confusion this caused. The advice from Hans-Rudolf is under normal circumstances the best first-pass route for troubleshooting, and you will want to restart after using the fasta method as well. Best, Jen Galaxy team On 1/28/14 11:12 AM, Yupu Liang wrote: Hi, I am trying to set up the visualization functionality on our local Galaxy installation. I followed the instructions on https://wiki.galaxyproject.org/Visualization%20Setup And here is the list of len files: ls -l tool-data/shared/ucsc/chrom/ total 200 -rw-rw-r-- 1 galaxy galaxy10 Jan 27 15:13 centromeres1.len -rw-rw-r-- 1 galaxy galaxy 821 Jan 27 15:13 hg15.len -rw-rw-r-- 1 galaxy galaxy 713 Jan 27 15:13 hg16.len -rw-rw-r-- 1 galaxy galaxy 792 Jan 27 15:13 hg17.len -rw-rw-r-- 1 galaxy galaxy 855 Jan 27 15:13 hg18.len -rw-rw-r-- 1 galaxy galaxy 202 Jan 27 15:13 hg19Haps.len -rwxr-xr-x 1 galaxy galaxy 1971 Jan 27 15:13 hg19.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hg19LggInv.len -rw-rw-r-- 1 galaxy galaxy 4516 Jan 27 15:13 hg19Patch10.len -rw-rw-r-- 1 galaxy galaxy 1983 Jan 27 15:13 hg19Patch2.len -rw-rw-r-- 1 galaxy galaxy 2844 Jan 27 15:13 hg19Patch5.len -rw-rw-r-- 1 galaxy galaxy 3879 Jan 27 15:13 hg19Patch9.len -rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef1.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef2.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef3.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase0.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase1.len -rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHuman.len -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHumanMammal.len -rw-rw-r-- 1 galaxy galaxy 362 Jan 27 15:13 venter1.len When I test the visualization through Trackster. I got the following error after seeing a message saying preparing the data, this can take a while……: Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or directory. It seems something else failed in the middle of visualization as I do have the hg18.len under the default path with the global reading permission…….. Does anybody have similar experience? Is there is way for me to debug? Best, Yupu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev
[galaxy-user] problem with scientific notation sorting and filtering in galaxy
I have found that numbers in scientific notation (e.g 9.8E-9) are incorrectly sorted or filtered by Galaxy. Looks like the negative exponent is ignored and so if you sorting something like P values (see example below) then you find these ordered above P=1 instead at the other end of the list where P is near zero. In the example below a KEGG list is ordered on column 5 in asending order by galaxy. If you scroll to the bottom of the list, however, you will see the smallest numbers all of which are in scientific notation. I should note that I can can copy this into excel and excel will properly sort scientific notation. So this seems to be a specific problem with Galaxy. I found this problem with both filtering and sorting functions of Galaxy. Doug Cavener 41 0.5326 1.0 0.025 cfa04146=Peroxisome 39 0.5325 1.0 0.038 cfa04640=Hematopoietic cell lineage 29 0.5913 1.0 0.044 cfa00980=Metabolism of xenobiotics by cytochrome P450 22 0.6310 1.0 0.16cfa00140=Steroid hormone biosynthesis 28 0.5619 1.0 0.27cfa05204=Chemical carcinogenesis 11 0.853 1.0 0.33cfa00511=Other glycan degradation 25 0.5716 1.0 0.52cfa00600=Sphingolipid metabolism 9 0.902 1.0 0.74cfa00740=Riboflavin metabolism 23 0.5814 1.0 0.79cfa00380=Tryptophan metabolism 15 0.686 1.0 0.96cfa04977=Vitamin digestion and absorption 22 0.5617 1.0 0.00017 cfa00071=Fatty acid metabolism 22 0.5617 1.0 0.00017 cfa05150=Staphylococcus aureus infection 26 0.5327 1.0 0.00017 cfa00982=Drug metabolism - cytochrome P450 49 0.4442 1.0 0.00018 cfa04142=Lysosome 56 0.4247 1.0 0.00024 cfa04630=Jak-STAT signaling pathway 34 0.4835 1.0 0.00026 cfa03320=PPAR signaling pathway 13 0.685 1.0 0.00027 cfa00531=Glycosaminoglycan degradation 20 0.5621 1.0 0.00043 cfa04975=Fat digestion and absorption 22 0.5424 1.0 0.00043 cfa00830=Retinol metabolism 19 0.5620 1.0 0.00053 cfa00565=Ether lipid metabolism 14 0.6111 1.0 0.00092 cfa00591=Linoleic acid metabolism 20 0.5328 1.0 0.0011 cfa02010=ABC transporters 22 0.5032 1.0 0.0015 cfa00280=Valine, leucine and isoleucine degradation 33 0.4444 1.0 0.0020 cfa04974=Protein digestion and absorption 15 0.5621 1.0 0.0022 cfa03440=Homologous recombination 14 0.5619 1.0 0.0028 cfa00650=Butanoate metabolism 35 0.4248 1.0 0.0035 cfa05323=Rheumatoid arthritis 16 0.5231 1.0 0.0043 cfa00350=Tyrosine metabolism 16 0.5231 1.0 0.0043 cfa05320=Autoimmune thyroid disease 12 0.5715 1.0 0.0044 cfa00592=alpha-Linolenic acid metabolism 15 0.5230 1.0 0.0054 cfa00760=Nicotinate and nicotinamide metabolism 21 0.4739 1.0 0.0054 cfa05144=Malaria 84 0.3666 1.0 0.0059 cfa04080=Neuroactive ligand-receptor interaction 16 0.4833 1.0 0.0091 cfa05143=African trypanosomiasis 12 0.5229 1.0 0.011 cfa00340=Histidine metabolism 14 0.4834 0.990.015 cfa05330=Allograft rejection 9 0.5618 1.0 0.015 cfa04614=Renin-angiotensin system 3 1.0 1 1.0 0.021 cfa00780=Biotin metabolism 35 0.3856 0.990.021 cfa00240=Pyrimidine metabolism 15 0.4443 0.990.030 cfa04940=Type I diabetes mellitus 11 0.4836 0.990.032 cfa00563=Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 29 0.3854 0.980.032 cfa04512=ECM-receptor interaction 20 0.4150 0.980.034 cfa04622=RIG-I-like receptor signaling pathway 9 0.5032 0.990.037 cfa00100=Steroid biosynthesis 10 0.4837 0.990.042 cfa04950=Maturity onset diabetes of the young 7 0.5423 0.990.042 cfa03450=Non-homologous end-joining 6 0.5522 0.990.055 cfa00430=Taurine and hypotaurine metabolism 6 0.5522 0.990.055 cfa00790=Folate biosynthesis 22 0.3858 0.970.060 cfa05140=Leishmaniasis 12 0.4346 0.970.062 cfa00512=Mucin type O-Glycan biosynthesis 3 0.754 0.990.068 cfa00061=Fatty acid biosynthesis 3 0.754 0.990.068 cfa00232=Caffeine metabolism 23 0.3762 0.960.070 cfa04115=p53 signaling pathway 29 0.3664 0.960.071 cfa00564=Glycerophospholipid metabolism 8 0.4738 0.980.071 cfa00120=Primary bile
[galaxy-user] special character $ gets converted to X in tool
Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI. Thanks, Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] special character $ gets converted to X in tool
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI. Thanks, Ketan This is a security feature I think - or it may just need escaping as \$ Since you are writing the script, why not pass in the environment variable name without the dollar? Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] February 2014 Galaxy Update Newsletter
Hello all, The 25th Edition of Galaxy Update is outhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02. Highlights from the February 2014 Galaxy Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02 include: - 42 new papershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#New_Papers - Who's hiringhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Who.27s_Hiring - Upcoming Eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Events, including - Registration for GCC2014 opens February 10https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#GCC2014:_June_30_-_July_2.2C_Baltimore - Registration for the Galaxy Australasia Workshop 2014 (GAW 2014)https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Australasia_Workshop_2014_.28GAW_2014.29 and GMOD Malaysia 2014https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#GMOD_Malaysia_2014 are open. - Three new public Galaxy servershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#New_Public_Servers - January 2014 CloudMan Releasehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Distributions - New Galaxy Deployment Cataloghttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Community_Hubs and Community Log Boardhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Community_Hubs entries - Tool Shed Contributionshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#ToolShed_Contributions - Johns Hopkins and George Washington walk into a bar ...https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_is_now_at_Johns_Hopkins_and_GWU_.28and_Penn_State.21.29 - Other Newshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Other_News If you have anything you would like to see in the next *Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Dave Clements and the Galaxy Teamhttps://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] GATK - Base recalibrator
Hi all, I'm trying to call variants using GATK best practices workflow. So after performing Realigner Target Creator step, one should jump on Base Recalibrator step. Unfortunatly, I don't see this program under GATK tab. Is there a way to perform this step in Galaxy? There are the Count covariates and Table recalibration steps. Is a combination of these two steps is equivalent to Base recalibrator? Thank you for your help and time. Frank ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] GATK - Base recalibrator
Hi Frank, Yes, that's equivalent; BaseRecalibrator is a single tool that combines those two steps in more recent versions. The version of GATK in Galaxy (1.6 afaik) is a pretty old one. I would strongly recommend using the most recent version of GATK (2.8) as it will give you better results. Good luck Geraldine On Fri, Jan 31, 2014 at 1:51 PM, Bolduc, Francois francois.bol...@usherbrooke.ca wrote: Hi all, I'm trying to call variants using GATK best practices workflow. So after performing Realigner Target Creator step, one should jump on Base Recalibrator step. Unfortunatly, I don't see this program under GATK tab. Is there a way to perform this step in Galaxy? There are the Count covariates and Table recalibration steps. Is a combination of these two steps is equivalent to Base recalibrator? Thank you for your help and time. Frank ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Geraldine A. Van der Auwera, Ph.D. Bioinformatics Scientist Broad Institute ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] problem with scientific notation sorting and filtering in galaxy
Hi Douglas, I encourage you and anyone else that has encountered this error to up-vote this issue in the Galaxy Trello board: https://trello.com/c/QZlmb0Yf That will help us prioritize work. Thanks for reporting this. Dave C On Thu, Jan 30, 2014 at 10:24 AM, Douglas Cavener d...@psu.edu wrote: I have found that numbers in scientific notation (e.g 9.8E-9) are incorrectly sorted or filtered by Galaxy. Looks like the negative exponent is ignored and so if you sorting something like P values (see example below) then you find these ordered above P=1 instead at the other end of the list where P is near zero. In the example below a KEGG list is ordered on column 5 in asending order by galaxy. If you scroll to the bottom of the list, however, you will see the smallest numbers all of which are in scientific notation. I should note that I can can copy this into excel and excel will properly sort scientific notation. So this seems to be a specific problem with Galaxy. I found this problem with both filtering and sorting functions of Galaxy. Doug Cavener 410.53261.00.025cfa04146=Peroxisome390.5325 1.00.038cfa04640=Hematopoietic cell lineage290.59131.00.044cfa00980=Metabolism of xenobiotics by cytochrome P450 220.63101.00.16cfa00140=Steroid hormone biosynthesis28 0.56191.00.27cfa05204=Chemical carcinogenesis 110.8531.00.33cfa00511=Other glycan degradation250.57161.00.52cfa00600=Sphingolipid metabolism 9 0.9021.00.74cfa00740=Riboflavin metabolism230.58141.00.79cfa00380=Tryptophan metabolism 150.6861.00.96cfa04977=Vitamin digestion and absorption22 0.56171.00.00017cfa00071=Fatty acid metabolism 220.56171.00.00017cfa05150=Staphylococcus aureus infection260.53271.00.00017cfa00982=Drug metabolism - cytochrome P450 490.44421.00.00018cfa04142=Lysosome560.42471.00.00024cfa04630=Jak-STAT signaling pathway 340.48351.00.00026cfa03320=PPAR signaling pathway130.685 1.00.00027cfa00531=Glycosaminoglycan degradation 200.56211.00.00043cfa04975=Fat digestion and absorption220.54241.00.00043cfa00830=Retinol metabolism 19 0.56201.00.00053cfa00565=Ether lipid metabolism140.6.00.00092cfa00591=Linoleic acid metabolism 200.53281.00.0011cfa02010=ABC transporters220.50321.0 0.0015cfa00280=Valine, leucine and isoleucine degradation 330.1.0 0.0020cfa04974=Protein digestion and absorption150.56211.00.0022cfa03440=Homologous recombination 140.56191.00.0028cfa00650=Butanoate metabolism350.42481.0 0.0035cfa05323=Rheumatoid arthritis 160.52311.00.0043cfa00350=Tyrosine metabolism160.52311.00.0043cfa05320=Autoimmune thyroid disease 120.57151.0 0.0044cfa00592=alpha-Linolenic acid metabolism150.52301.00.0054cfa00760=Nicotinate and nicotinamide metabolism 210.47391.00.0054cfa05144=Malaria840.36661.0 0.0059cfa04080=Neuroactive ligand-receptor interaction 160.48331.00.0091cfa05143=African trypanosomiasis120.52291.00.011cfa00340=Histidine metabolism 140.48340.99 0.015cfa05330=Allograft rejection90.56181.00.015cfa04614=Renin-angiotensin system 31.011.00.021cfa00780=Biotin metabolism350.38560.990.021cfa00240=Pyrimidine metabolism15 0.44430.990.030cfa04940=Type I diabetes mellitus110.48360.99 0.032cfa00563=Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 290.38 540.980.032cfa04512=ECM-receptor interaction200.41500.980.034cfa04622=RIG-I-like receptor signaling pathway 90.50320.990.037cfa00100=Steroid biosynthesis10 0.48370.990.042cfa04950=Maturity onset diabetes of the young 70.54230.99 0.042cfa03450=Non-homologous end-joining60.55220.990.055cfa00430=Taurine and hypotaurine metabolism 60.55220.990.055cfa00790=Folate biosynthesis22 0.38580.970.060cfa05140=Leishmaniasis 120.43460.970.062cfa00512=Mucin type O-Glycan biosynthesis30.7540.990.068cfa00061=Fatty acid biosynthesis 30.7540.990.068cfa00232=Caffeine metabolism230.37620.960.070cfa04115=p53 signaling pathway 290.36640.960.071cfa00564=Glycerophospholipid metabolism 80.47380.980.071cfa00120=Primary bile acid biosynthesis 200.38590.960.074cfa00561=Glycerolipid metabolism190.38570.960.076cfa04612=Antigen processing and presentation 48 0.34740.950.076cfa05152=Tuberculosis180.38530.960.077cfa00510=N-Glycan biosynthesis 21.011.00.077cfa00290=Valine, leucine and isoleucine biosynthesis160.39520.960.079cfa00500=Starch and sucrose metabolism 160.39 520.960.079cfa04621=NOD-like receptor signaling pathway120.41490.960.080cfa00410=beta-Alanine metabolism 70.47390.970.093cfa00604=Glycosphingolipid biosynthesis - ganglio series330.34720.940.094cfa05146=Amoebiasis 80.44410.960.097cfa00900=Terpenoid backbone biosynthesis40.57150.980.099cfa00460=Cyanoamino acid metabolism 4 0.57150.980.099cfa00750=Vitamin B6 metabolism120.40510.950.10cfa00052=Galactose metabolism 120.40510.950.10cfa00983=Drug metabolism - other enzymes90.4346 0.960.10cfa00040=Pentose and glucuronate interconversions 50.50320.970.11cfa04122=Sulfur relay system260.35700.930.12cfa04064=NF-kappa B signaling
Re: [galaxy-user] special character $ gets converted to X in tool
Thanks! Just wanted to report that \$ does not work; \ adds one more X. On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI. Thanks, Ketan This is a security feature I think - or it may just need escaping as \$ Since you are writing the script, why not pass in the environment variable name without the dollar? Peter -- Ketan ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
