[galaxy-dev] double check for EMS Variant Density Mapping
Dear folks, Could you help me double check if my understanding is correct for EMS density mapping? For the tool CloudMap: EMS Variant Density Mapping, it does not work for other species except C.elegans, correct? For the workflow CloudMap EMS Variant Density Mapping workflow (takes VCF of heterozygous and homozygous variants to subtract) in published workflows, the final step is to plot the VCF output using the tool CloudMap: EMS Variant Density Mapping. If I want to use this workflow on other species, I need to remove this tool/step from the workflow by edit it. If I do not remove this step, there is nothing in the output of EMS Variant Density plot even the color is green for this step in the history, right? Thanks a lot! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
Dear folks, Why could not I find BDGP 5.74 in the drop-down menu of SnpEff? If I want to use this version, what should I do or what other steps do I need to install it? Thank you so much! From: Wang, Xiaofei Sent: Monday, April 14, 2014 9:50 AM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Dear there, Could someone tell me why there is no Drosophila melanogaster : BDGP 5.74 in the drop-down menu of SnpEff for local Galaxy? In fact, I could find it (BDGP 5.74) in SnpEff Databases and also download it from SnpEff Download (Data manager: Admin Manage local data (beta)). But, I still can not find it in the menu of SnpEff after downloading and installing it by the two-steps as below. Thanks a lot! Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Friday, April 11, 2014 5:52 PM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors I am sorry to bother again about this problem. I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the Genome drop-down menu in SnpEff. The version of SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.) Thanks Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 3:52 PM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Oh, hooray, I figured it out. what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again: java -jar snpEff.jar download dm5.42 Thank you so much! Best, Xiaofei _ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 10:31 AM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value name path dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Dear there, Could someone tell me why there is no Drosophila melanogaster : BDGP 5.74 in the drop-down menu of SnpEff for local Galaxy? In fact, I could find it (BDGP 5.74) in SnpEff Databases and also download it from SnpEff Download (Data manager: Admin Manage local data (beta)). But, I still can not find it in the menu of SnpEff after downloading and installing it by the two-steps as below. Thanks a lot! Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Friday, April 11, 2014 5:52 PM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors I am sorry to bother again about this problem. I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the Genome drop-down menu in SnpEff. The version of SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.) Thanks Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 3:52 PM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Oh, hooray, I figured it out. what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again: java -jar snpEff.jar download dm5.42 Thank you so much! Best, Xiaofei _ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 10:31 AM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value name path dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list
[galaxy-dev] an error to SnpEff (CloudMap)
Dear there, I got this error as below when I run CloudMap workflow in local galaxy instance. What is it the meaning of this error? Is it a general error or specific one for my data? Thanks a lot! Xiaofei error An error occurred with this dataset: WARNINGS: Some warning were detected Warning typeNumber of warnings WARNING_TRANSCRIPT_INCOMPLETE 36 WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS 18 WARNING_TRANSCRIPT_NO_START_CODON 100 ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] how to delete datasets or save space on local galaxy
Hi Carl, The size is changed when the page is reloaded. Here is how I purge the data: 1. Mark them deleted using the X button on the dataset 2. From the history options menu, select 'Purge Deleted Datasets' I think this will purge the deleted datasets too (correct?) because in the yellow box it shows that This dataset has been deleted and removed from disk. But I am not sure if there is any difference with the 3-steps that you advised. I think the difference might be that it can purge the dataset one by one in your advice, is it? Thanks Xiaofei From: Carl Eberhard [carlfeberh...@gmail.com] Sent: Monday, April 14, 2014 8:47 AM To: Wang, Xiaofei Cc: Dannon Baker; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hello, That's a good question! Does the size in the top right change when the page is reloaded? Are these datasets copied from another history? How are you purging the datasets? As Dannon mentioned, if you click the 'X' button on the dataset it will 'mark' the dataset as deleted. To permanently deleted the datasets (or 'purge' them), you can: 1. Mark them deleted using the 'X' button on the dataset, 2. Then from the history options menu (the button that looks like a gear at the top of the history), select 'Include deleted datasets'. This will make the dataset you marked as deleted visible in the history again. 3. In the deleted dataset you'll see a yellow box explaining that the history has been deleted and showing two links: one for undeleting the dataset (which will undo the deletion of the dataset) and one for immediately removing it from disk - this link will purge the dataset. Click the second link. You can hide the deleted datasets again by clicking: history options menu - 'Include deleted datasets' again. If you do the above, does the size in the top right change or still remain the same? Let me know if you need more info, Carl On Fri, Apr 11, 2014 at 6:25 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? From: Dannon Baker [dannon.ba...@gmail.commailto:dannon.ba...@gmail.com] Sent: Friday, April 11, 2014 4:57 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com wrote: Hey, sure. The option you're looking for is allow_user_dataset_purge, around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei From: Dannon Baker [dannon.ba...@gmail.commailto:dannon.ba...@gmail.com] Sent: Friday, April 11, 2014 4:42 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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
[galaxy-dev] how to delete datasets or save space on local galaxy
Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei inline: Screen Shot 2014-04-11 at 4.30.18 PM.png___ Please keep all replies on the list by using reply all in your mail client. 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-dev] how to delete datasets or save space on local galaxy
Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei From: Dannon Baker [dannon.ba...@gmail.com] Sent: Friday, April 11, 2014 4:42 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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/ inline: Screen Shot 2014-04-11 at 4.30.18 PM.png___ Please keep all replies on the list by using reply all in your mail client. 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-dev] how to delete datasets or save space on local galaxy
Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? From: Dannon Baker [dannon.ba...@gmail.com] Sent: Friday, April 11, 2014 4:57 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com wrote: Hey, sure. The option you're looking for is allow_user_dataset_purge, around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei From: Dannon Baker [dannon.ba...@gmail.commailto:dannon.ba...@gmail.com] Sent: Friday, April 11, 2014 4:42 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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/ inline: Screen Shot 2014-04-11 at 4.30.18 PM.png___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
I am sorry to bother again about this problem. I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the Genome drop-down menu in SnpEff. The version of SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.) Thanks Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 3:52 PM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Oh, hooray, I figured it out. what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again: java -jar snpEff.jar download dm5.42 Thank you so much! Best, Xiaofei _ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 10:31 AM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value name path dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list of available genomes that in a next step is shown under the tool SnpEff Databases there you can choose which genome annotation you want to install. To sum it up. 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? Then there is something missing from your reinstallation. The data manager is a dependency of the snpeff package and should be installed as well. Can you check if you need
[galaxy-dev] Download workflow from main Galaxy
Dear there, I tried to download workflow and import it into another my local Galaxy instance. But, when I downloaded and exported it from main Galaxy by Download to File, it showed as below. Not Found The resource could not be found. No route for /u/w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json-download Then, I tried URL for Importing to Another Galaxy Use this URL to import the workflow directly into another Galaxy server: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json (Copy this URL into the box titled 'Workflow URL' in the Import Workflow page.) , it showed Failed to open URL: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json Exception: HTTP Error 404: Not Found What is the reason for this? Many thanks for helping me! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] Download workflow from main Galaxy
Yes, I really appreciate for your help! From: emulato...@gmail.com [emulato...@gmail.com] on behalf of Martin Čech [mar...@bx.psu.edu] Sent: Friday, April 04, 2014 11:28 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Download workflow from main Galaxy Hello Xiaofei, it seems you don't have username set in usegalaxy.orghttp://usegalaxy.org and thus the links generated are wrong. Can you please set one (user/preferences/manage information) and try again? thanks Martin Galaxy team On Fri, Apr 4, 2014 at 12:07 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, I tried to download workflow and import it into another my local Galaxy instance. But, when I downloaded and exported it from main Galaxy by Download to File, it showed as below. Not Found The resource could not be found. No route for /u/w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json-download Then, I tried URL for Importing to Another Galaxy Use this URL to import the workflow directly into another Galaxy server: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json (Copy this URL into the box titled 'Workflow URL' in the Import Workflow page.) , it showed Failed to open URL: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json Exception: HTTP Error 404: Not Found What is the reason for this? Many thanks for helping me! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] version of SAM-to-BAM (CloudMap)
Yes, it is figured out when I downloaded the version of 1.1.2. I thought is no longer available. Thank you so much! Best, Xiaofei From: Nate Coraor [n...@bx.psu.edu] Sent: Friday, April 04, 2014 11:20 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] version of SAM-to-BAM (CloudMap) Hi Xiaofei, You should be able to install 1.1.3 by selecting revision 3 of sam_to_bam from the Preview and install page (Admin - Search and browse tool sheds - Galaxy main tool shed - sam_to_bam - Preview and install), and then clicking Install to Galaxy. [Inline image 1] You can tell what version of the tool it'll install by looking at the Valid tools section of the Contents of this repository box. --nate On Thu, Apr 3, 2014 at 6:16 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of heterozygous and homozygous variants to subtract) (imported from uploaded file) on local Galaxy instance, I got this [X] , when I wanted to edit the workflow. Also, I got this The following tools are beinge executed with a different version from what was available when this workflow was last saved because the previous version is no longer available for use on this galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it to update the stored tool version. * toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2http://toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2: using version '1.1.2' instead of version '1.1.3' indicated in this workflow. * ,when I wanted to run the workflow. I know it is the problem with version of SAM-to-BAM. But, when I searched the Tool sheds Search and browse tool sheds, there is only version 1.1.4 for SAM-to-BAM. When I tried to edit the workflow from Workflow ... Edit, I did not find where could I change the version of SAM-to-BAM. When I clicked on SAM-to-BAM on the Workflow Canvas, it showed the version is 1.1.3 for it. Could you tell me which version do I need exactly, and how to figure out this? Thanks a lot! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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/ inline: sam_to_bam_3.png___ Please keep all replies on the list by using reply all in your mail client. 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-dev] Depth of Coverage (local galaxy __ CloudMap)
Dear there, I got this error when I run CloudMap EMS Variant Density Mapping workflow for Depth of Coverage on the local Galaxy instance on Mac. In fact, it works fine for Depth of Coverage when I run another workflow (Unmapped Mutant workflow) locally. I really appreciate you guys for helping me to figure out so many problems! Thanks a lot! Best, Xiaofei Traceback (most recent call last): File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 152, in prepare_job job_wrapper.prepare() File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/__init__.py, line 652, in prepare if job.user is None and job.galaxy_session is None: File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py, line 168, in __get__ return self.impl.get(instance_state(instance),dict_) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py, line 453, in get value = self.callable_(state, passive) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py, line 508, in _load_for_state return self._emit_lazyload(session, state, ident_key) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py, line 552, in _emit_lazyload return q._load_on_ident(ident_key) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py, line 2512, in _load_on_ident return q.one() File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py, line 2184, in one ret = list(self) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py, line 2227, in __iter__ return self._execute_and_instances(context) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py, line 2242, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py, line 1449, in execute params) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py, line 1584, in _execute_clauseelement compiled_sql, distilled_params File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py, line 1698, in _execute_context context) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File /Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) database is locked u'SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token \nFROM galaxy_user \nWHERE galaxy_user.id = ?' (1,) ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value namepath dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list of available genomes that in a next step is shown under the tool SnpEff Databases there you can choose which genome annotation you want to install. To sum it up. 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? Then there is something missing from your reinstallation. The data manager is a dependency of the snpeff package and should be installed as well. Can you check if you need to reinstall the dependency manually unter the snpeff tool in your admin panel? Cheers, Bjoern When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. After SnpEff Databases Execute you still need to pick genome
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Dear there, I am still stuck there for FASTQ Summary Statistics. Could you give me some clues to fix it? Thanks a lot! Best, Xiaofei From: Wang, Xiaofei Sent: Wednesday, April 02, 2014 11:21 AM To: Daniel Blankenberg Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Oh, yes, here it is: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in module if __name__ == __main__: main() File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 32, in main base_counts = aggregator.get_base_counts_for_column( i ) File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py, line 397, in get_base_counts_for_column return self.nuc_index_base[ column ] IndexError: list index out of range From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, April 02, 2014 11:14 AM To: Wang, Xiaofei Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane? Thanks for using Galaxy, Dan On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei xfw...@ku.edu wrote: Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
Oh, hooray, I figured it out. what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again: java -jar snpEff.jar download dm5.42 Thank you so much! Best, Xiaofei _ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, April 03, 2014 10:31 AM To: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is: java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download dm5.42 at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem? May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times): Data Manager: snpeff_genomedb value namepath dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Thursday, April 03, 2014 5:25 AM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Am 03.04.2014 04:34, schrieb Wang, Xiaofei: After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. It's a little bit complicated. If you click on the SnpEff Download under Data Manager a progress ist started that will fetch a list of available genomes that in a next step is shown under the tool SnpEff Databases there you can choose which genome annotation you want to install. To sum it up. 1. click SnpEff Download 2. choose one genome from SnpEff Databases and install it Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? Then there is something missing from your reinstallation. The data manager is a dependency of the snpeff package and should be installed as well. Can you check if you need to reinstall the dependency manually unter the snpeff tool in your admin panel? Cheers, Bjoern When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff
[galaxy-dev] version of SAM-to-BAM (CloudMap)
Dear there, When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of heterozygous and homozygous variants to subtract) (imported from uploaded file) on local Galaxy instance, I got this [X] , when I wanted to edit the workflow. Also, I got this The following tools are beinge executed with a different version from what was available when this workflow was last saved because the previous version is no longer available for use on this galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it to update the stored tool version. * toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2: using version '1.1.2' instead of version '1.1.3' indicated in this workflow. * ,when I wanted to run the workflow. I know it is the problem with version of SAM-to-BAM. But, when I searched the Tool sheds Search and browse tool sheds, there is only version 1.1.4 for SAM-to-BAM. When I tried to edit the workflow from Workflow ... Edit, I did not find where could I change the version of SAM-to-BAM. When I clicked on SAM-to-BAM on the Workflow Canvas, it showed the version is 1.1.3 for it. Could you tell me which version do I need exactly, and how to figure out this? Thanks a lot! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
Oh, yes, here it is: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in module if __name__ == __main__: main() File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 32, in main base_counts = aggregator.get_base_counts_for_column( i ) File /Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py, line 397, in get_base_counts_for_column return self.nuc_index_base[ column ] IndexError: list index out of range From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, April 02, 2014 11:14 AM To: Wang, Xiaofei Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane? Thanks for using Galaxy, Dan On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei xfw...@ku.edu wrote: Can you give us the complete error message. The important part is missing. Here is the whole thing for the error: Traceback (most recent call last): File /Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/xiaofe I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for FASTQ Summary Statistics or CloundMap? Thanks a lot! From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Yes, it is figured, when I changed the java version to 1.7. Thank you so much! But, I got another error for snpEff. java.lang.RuntimeException: Property: 'dm5.30.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.init(Genome.java:92) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:96) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply. Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? ) param name=genomeVersion type=select label=Genome option value=hg37Human (hg37)option option value=mm37.61Mouse (mm37.61)option param From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 10:35 AM To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Which Java version do you use. Please make sure you are running Java 1.7. Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File /Users/./softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py, line 48, in if __name__ == __main__: main() File /Users/... Can you give us the complete error message. The important part is missing. Ciao, Bjoern I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help! ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] snpEff and FASTQ Summary Statistics errors
Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databaseshttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4 - Download a new database * BWA indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by manager * SnpEff Databaseshttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1 - Download a new database * BWA indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by Tool Data Table * snpeff_databaseshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases * snpeff_genomedbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb * snpeff_regulationdbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb * snpeff_annotationshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations * bwa_indexeshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes * bwa_indexes_colorhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color * all_fastahttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta * * * * * From: Björn Grüning [bjoern.gruen...@gmail.com] * Sent: Wednesday, April 02, 2014 12:55 PM * To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors * * Hi, * * that means that the snpeff annotation is missing. You can install it * with the snpeff datamanager under your Admin panel. Have a look at the * wiki page about data-manager and the snpeff wrapper documentation. * You do not need to edit xml files. If so that is an bug in the wrapper * and we should fix it :) * * Cheers, * Bjoern * * Am 02.04.2014 19:34, schrieb Wang, Xiaofei: *When I used SnpEff in local galaxy instance, I got an error: *Exception in thread main java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j * * * * *Which Java version do you use. Please make sure you are running Java 1.7. * * * * *Yes, it is figured, when I changed
Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. You mean SnpEff Download under Data Manager? But, there is no response when I click on it. Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin Data Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why? When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time? Thank you so much! Best, Xiaofei From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, April 02, 2014 4:17 PM To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors Hi Xiaofei, Dear Bjoern, As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is: Admin Data Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. After SnpEff Databases Execute you still need to pick genome of interest and run SnpEff Download. SnpEff Databases just downloads a list of available genomes. Hope that will help! Bjoern Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel? I really appreciate for your help, and thank you so much for your patience! Best, Xiaofei Data Manager Choose your data managing option from below. * Access data managers - get data, build indexes, etc * SnpEff Databaseshttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4 - Download a new database * BWA indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by manager * SnpEff Databaseshttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1 - Read the list of available snpEff databases * SnpEff Downloadhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1 - Download a new database * BWA indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1 - builder * BWA Color indexhttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1 - builder * Reference Genomehttp://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1 - fetching * View managed data by Tool Data Table * snpeff_databaseshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases * snpeff_genomedbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb * snpeff_regulationdbhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb * snpeff_annotationshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations * bwa_indexeshttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes * bwa_indexes_colorhttp://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color
Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)
Hi Greg, I figured it out. I forgot to check the box Check to uninstall or leave blank to deactivate . I need to uninstall the tool shed but I leave the box blank firstly. So, it is not uninstalled but just deactivated. Thank you so much! From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, March 11, 2014 8:47 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) Hello, It's difficult to determine the cause of the problem in your environment based on the details you've provided. If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there. If you see them installed elsewhere, then that setting must have been set differently at the time they were installed. You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them. Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them. If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location. Greg Von Kuster On Mar 6, 2014, at 5:41 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing. Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20DependenciesToolhttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies%20Dependencieshttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin manage installed tool shed repositories, the installation status is Installed, missing tool dependencies for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread The migrated BWA installed but missing dependencies. But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! -- Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] tool_sheds_errors
Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file '~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I copied the four files from ~/.../script folder. Now, this tool works. But, I don't think this is a right way to figure out this because I also got similar problem (I think they are similar) when I used other tool sheds as below. So, I am guessing it might be a problem with my configure file (universe_wsgi.ini). Could anybody tell me why and how to figure it out? BWA wrapper error: when I used the BWA wrapper for Illunina, An error occurred with this dataset: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found I referred to this link to try to figure out the problem http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. But, I think I need more details about the mentioned bwa binaries and path. When I used the snpEff, the error is: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar In fact, the snpEff.jar is located at ~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a Could you give me some ideas? Thank you so much! From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, March 11, 2014 8:47 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) Hello, It's difficult to determine the cause of the problem in your environment based on the details you've provided. If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there. If you see them installed elsewhere, then that setting must have been set differently at the time they were installed. You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them. Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them. If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location. Greg Von Kuster On Mar 6, 2014, at 5:41 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing. Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20DependenciesToolhttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies%20Dependencieshttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin manage installed tool shed repositories, the installation status is Installed, missing tool dependencies for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread The migrated BWA installed but missing dependencies. But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! -- Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting
Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)
Hi folks, Could anybody answer my question and help me figure it out? Thank you so much! Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, March 06, 2014 4:41 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing. Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin manage installed tool shed repositories, the installation status is Installed, missing tool dependencies for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread The migrated BWA installed but missing dependencies. But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! -- Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] tool_dependency_dir (Installed, missing tool dependencies)
Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing. Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin manage installed tool shed repositories, the installation status is Installed, missing tool dependencies for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread The migrated BWA installed but missing dependencies. But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! -- Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] Reference Genome in snpEff Tool
I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Clint Christensen [cli...@txbiomedgenetics.org] Sent: Monday, February 17, 2014 10:01 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Reference Genome in snpEff Tool Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.org ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)
Dear, Is it possible to use SnpEff with genomes of other species (e.g. Drosophila) other than C.elegan on galaxy website (not local)? It seems the only option for the genome menu (Caenorhabditis elegants : WS220.64). In fact, I am trying to use CloudMap (the EMS Variant Density Mapping workflow) to analyze data for Drosophila. So, I have to edit the workflow based on my own data. For SnpEff on the workflow, I tried to change Genome to other species from Caenorhabditis elegants : WS. But, there is no other options. Then, I changed it to be set at runtime. When I run the workflow, I still can not change it to other species. Then, I went to see the SnpEff tool on galaxy website and found that there is no other options for Genome option. So, could you help me about this? Could I use SnpEff and CloudMap (the EMS Variant Density Mapping workflow) other than worm? Or, I have to install galaxy locally for this objective? Thank you so much! Have a nice day! ___ Please keep all replies on the list by using reply all in your mail client. 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-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)
Thank you so much for your reply! But, may I double check what do you mean by try the Mapping tool individually? maybe try the Mapping tool individually first with some test data to see whether you are getting any result at all. You mean I should try the tools individually (like BWA for map, GATK for calling SNPs, ...) by hand not use the CloudMap pipeline on Drosophila? Thanks From: Wolfgang Maier [wolfgang.ma...@biologie.uni-freiburg.de] Sent: Friday, February 14, 2014 11:48 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local) Last time I checked the EMS Variant Density Mapping tool, specifically, had an unnecessary restriction to chromosome names as in WS220.64 (chrI, chrII, chrIII, chrIV, chrV, chrX). So maybe before putting too much effort into the SnpEff side of the workflow, maybe try the Mapping tool individually first with some test data to see whether you are getting any result at all. Best, Wolfgang From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Wang, Xiaofei Sent: Friday, February 14, 2014 6:40 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local) Dear, Is it possible to use SnpEff with genomes of other species (e.g. Drosophila) other than C.elegan on galaxy website (not local)? It seems the only option for the genome menu (Caenorhabditis elegants : WS220.64). In fact, I am trying to use CloudMap (the EMS Variant Density Mapping workflow) to analyze data for Drosophila. So, I have to edit the workflow based on my own data. For SnpEff on the workflow, I tried to change Genome to other species from Caenorhabditis elegants : WS. But, there is no other options. Then, I changed it to be set at runtime. When I run the workflow, I still can not change it to other species. Then, I went to see the SnpEff tool on galaxy website and found that there is no other options for Genome option. So, could you help me about this? Could I use SnpEff and CloudMap (the EMS Variant Density Mapping workflow) other than worm? Or, I have to install galaxy locally for this objective? Thank you so much! Have a nice day! ___ Please keep all replies on the list by using reply all in your mail client. 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/
