[galaxy-user] Dear Galaxy Developer, where is the history/workflow file stored in the local machine?
Dear Galaxy Developer, where is the history/workflow file stored in the local machine? I mean the real file store in the disk instead of browser access. Thanks and Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375___ 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/
[galaxy-user] Combining two workflows into one
Galaxy Team, I would like to create a workflow by combining portions of two different workflows. How do I do this in Galaxy? Thanks, Getiria Onsongo ___ 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/
Re: [galaxy-user] Combining two workflows into one
You forgot to CC the mailin list. On Mon, Mar 19, 2012 at 12:02 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Mar 19, 2012 at 4:53 PM, Innocent Onsongo onson...@umn.edu wrote: Galaxy Team, I would like to create a workflow by combining portions of two different workflows. How do I do this in Galaxy? Thanks, Getiria Onsongo One outline solution is as follows: (1) Start with an empty history. (2) Upload/import the input files (3) Run first workflow (4) Run second workflow (5) Save history as a new combined workflow (6) Edit new workflow to remove any redundant steps This is of course limited in functionality compared to what might be possible in a future version of Galaxy. Peter On Mon, Mar 19, 2012 at 5:05 PM, Innocent Onsongo onson...@umn.edu wrote: I was hoping I could avoid re-running the two workflows since they both take a relatively long time to run. Looks like I might have to do it after all. Use smaller datasets? Ideally you would have a small test set covering positive and negative example. Or you can manually create the workflow in the workflow editor, starting from one of the existing ones and adding the new tools and connecting them together. 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/
Re: [galaxy-user] Combining two workflows into one
Thanks. I was hoping there was an easier way e.g., selecting the two workflows and exporting them into a workflow canvas. The workflows are not too big so manually creating the workflows will probably be the faster option for now. On Mon, Mar 19, 2012 at 12:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote: You forgot to CC the mailin list. On Mon, Mar 19, 2012 at 12:02 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Mar 19, 2012 at 4:53 PM, Innocent Onsongo onson...@umn.edu wrote: Galaxy Team, I would like to create a workflow by combining portions of two different workflows. How do I do this in Galaxy? Thanks, Getiria Onsongo One outline solution is as follows: (1) Start with an empty history. (2) Upload/import the input files (3) Run first workflow (4) Run second workflow (5) Save history as a new combined workflow (6) Edit new workflow to remove any redundant steps This is of course limited in functionality compared to what might be possible in a future version of Galaxy. Peter On Mon, Mar 19, 2012 at 5:05 PM, Innocent Onsongo onson...@umn.edu wrote: I was hoping I could avoid re-running the two workflows since they both take a relatively long time to run. Looks like I might have to do it after all. Use smaller datasets? Ideally you would have a small test set covering positive and negative example. Or you can manually create the workflow in the workflow editor, starting from one of the existing ones and adding the new tools and connecting them together. Peter -- Getiria Onsongo, Ph.D. Bioinformatics Research Scientist Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455 Phone: 612-625-0101 ___ 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/
[galaxy-user] Cuffdiff result P and q values
Dear galaxy user After running cuffdiff on my two samples (SAM files from bowtie) i got a list with p and q values, and löast colum is saying abou significance with P value, it seems like the comparison should be significant, but in Q value is 1, and last coumn is saying not significant any one have an idea, how to interpret it , should we take any comparsion with less than 0.05 p value as significant or not tables in excel looks like it Nay help is welcome best Ateeq test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant CUFF.428.1 CUFF.428 - gi|190572091|ref|NC_010943.1|:1575813-1577629 q1 q2 NOTEST 171.773 605.136 -150.518 588.996 3,86E-05 1 no CUFF.462.1 CUFF.462 - gi|190572091|ref|NC_010943.1|:1680283-1681214 q1 q2 NOTEST 696.628 322.149 -111.266 538.062 7,42E-03 1 no CUFF.635.1 CUFF.635 - gi|190572091|ref|NC_010943.1|:2343969-2346219 q1 q2 NOTEST 396.469 223.951 -0.824027 476.902 1,85E-01 1 no CUFF.512.1 CUFF.512 - gi|190572091|ref|NC_010943.1|:1840464-1843486 q1 q2 NOTEST 136.314 70.604 -0.949109 422.322 2,41E-01 1 no CUFF.632.1 CUFF.632 - gi|190572091|ref|NC_010943.1|:2346561-2347408 q1 q2 NOTEST 351.508 167.567 -106.882 415.844 3,20E-01 1 no CUFF.941.1 CUFF.941 - gi|190572091|ref|NC_010943.1|:3664426-3665364 q1 q2 NOTEST 282.247 133.798 -10.769 412.254 3,75E-01 1 no CUFF.616.1 CUFF.616 - gi|190572091|ref|NC_010943.1|:2301552-2303180 q1 q2 NOTEST 169.682 744.885 -118.774 462.107 3,82E-01 1 no CUFF.617.1 CUFF.617 - gi|190572091|ref|NC_010943.1|:2295763-2297758 q1 q2 NOTEST 225.933 112.178 -101.011 454.517 5,49E-01 1 no CUFF.9.1 CUFF.9 - gi|190572091|ref|NC_010943.1|:41597-42402 q1 q2 OK 1729.08 2797.07 0.693913 -4.461 8,16E-01 0.000179474 yes CUFF.956.1 CUFF.956 - gi|190572091|ref|NC_010943.1|:3665445-3669232 q1 q2 NOTEST 518.525 323.653 -0.679966 444.565 8,76E-01 1 no CUFF.549.1 CUFF.549 - gi|190572091|ref|NC_010943.1|:2043111-2043664 q1 q2 OK 7148.23 11816.4 0.725138 -421.443 2,50E+00 0.000275446 yes CUFF.872.1 CUFF.872 - gi|190572091|ref|NC_010943.1|:3489557-3490326 q1 q2 NOTEST 220.274 840.662 -13.897 416.179 3,16E+00 1 no CUFF.636.1 CUFF.636 - gi|190572091|ref|NC_010943.1|:2348784-2352394 q1 q2 NOTEST 114.384 601.415 -0.927447 414.807 3,35E+00 1 no CUFF.605.1 CUFF.605 - gi|190572091|ref|NC_010943.1|:2271979-2275960 q1 q2 NOTEST 217.007 133.837 -0.697264 409.373 4,24E+00 1 no CUFF.568.1 CUFF.568 - gi|190572091|ref|NC_010943.1|:2160538-2164415 q1 q2 NOTEST 74.365 377.013 -0.980011 395.097 7,78E+00 1 no CUFF.597.1 CUFF.597 - gi|190572091|ref|NC_010943.1|:2250029-2250918 q1 q2 NOTEST 229.389 105.246 -112.403 386.937 0.000109116 1 no Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau___ 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/
