Re: [galaxy-dev] API keys and id encryption (silly questions)
Le 29/08/2011 18:54, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Hi L-A, To provide a username password, we'd either need to implement HTTP Authentication in Galaxy for these resources, or encode it in the URL. If in the URL, the password have to be non-plaintext which would require encoding on the user's end. The key model seemed to be simplest since it doesn't require you to handle HTTP Authentication in your client-side code. Ok, I actually missed the point, thanks! :D Also, why encrypt the dataset/library/folder ids when a simple display is enough to get them? Anywhere that the IDs are visible are remnants of old code and should eventually be removed. Sorry I meant the encrypted ids. Why encrypt them? is it to prevent any direct use of the database? There are a couple of reasons - the first is that since by default, data is public, we wanted to make it non-trivial to just run sequentially through IDs to view related data. The other is that some people may prefer that it not be obvious how many datasets/jobs/libraries/etc. there are on their server. Ok, thanks a lot for all this information! :) Best, L-A --nate Thanks, L-A --nate Thanks L-A ___ 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/ ___ 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/
[galaxy-dev] set metadata step
Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? -- Thanks, Shantanu. ___ 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/
Re: [galaxy-dev] set metadata step
Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi Shantanu, Metadata is always detected/set on all job outputs. This setting simply controls whether the metadata setting occurs within the Galaxy server process or in a new process. It's highly recommended to always set this = True, and it will probably become the default in the future. --nate -- Thanks, Shantanu. ___ 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/ ___ 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/
Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy
I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that? Hi L-A, Pass in as an argument: $__app__.security.encode_id( 'file.%s' % $input1.id ) Where 'input1' is the param name of your input. --nate ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] set metadata step
On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi Shantanu, Metadata is always detected/set on all job outputs. This setting simply controls whether the metadata setting occurs within the Galaxy server process or in a new process. It's highly recommended to always set this = True, and it will probably become the default in the future. --nate Thanks Nate. So is this something in the core galaxy code and independent of tool wrappers? -- Shantanu. ___ 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/
Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy
Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents are all identified by ID, so: http://server/api/libraries/library_id/contents/content_id That content ID can refer to a dataset (file) or folder, but if this was not 'file.id' or 'folder.id', when the framework decoded it, it would just get a numeric ID and wouldn't know to which type it refered. So instead of using just the ID, it uses the encoded form of 'file.id' and 'folder.id'. This was extended to histories even though there isn't a concept of folders in histories. So just encoding the ID is going to give you the encoded HistoryDatasetAssociation id, but that ID won't be the dataset's API id. For example, using the default id_secret in universe_wsgi.ini, if I upload a dataset to a fresh instance of Galaxy, its encoded ID (the encoded value of '1') is: f2db41e1fa331b3e As you can see in the 'display' URL for the dataset: http://server/datasets/f2db41e1fa331b3e/display/ But that ID won't work for the history API: % ./display.py key http://server/api/histories/f597429621d6eb2b/contents Collection Members -- #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e name: 1.bed type: file id: cc1c6c1afcb4fd4e f597429621d6eb2b is the encoding of '2' with the default id_secret since this dataset is in history ID 2. cc1c6c1afcb4fd4e is the encoding of 'file.1'. --nate Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that? Hi L-A, Pass in as an argument: $__app__.security.encode_id( 'file.%s' % $input1.id ) Where 'input1' is the param name of your input. --nate ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] set metadata step
Shantanu Pavgi wrote: On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi Shantanu, Metadata is always detected/set on all job outputs. This setting simply controls whether the metadata setting occurs within the Galaxy server process or in a new process. It's highly recommended to always set this = True, and it will probably become the default in the future. --nate Thanks Nate. So is this something in the core galaxy code and independent of tool wrappers? Yes. It runs after the tool has finished executing. -- Shantanu. ___ 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/
Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy
Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents are all identified by ID, so: http://server/api/libraries/library_id/contents/content_id That content ID can refer to a dataset (file) or folder, but if this was not 'file.id' or 'folder.id', when the framework decoded it, it would just get a numeric ID and wouldn't know to which type it refered. So instead of using just the ID, it uses the encoded form of 'file.id' and 'folder.id'. This was extended to histories even though there isn't a concept of folders in histories. So just encoding the ID is going to give you the encoded HistoryDatasetAssociation id, but that ID won't be the dataset's API id. For example, using the default id_secret in universe_wsgi.ini, if I upload a dataset to a fresh instance of Galaxy, its encoded ID (the encoded value of '1') is: f2db41e1fa331b3e As you can see in the 'display' URL for the dataset: http://server/datasets/f2db41e1fa331b3e/display/ But that ID won't work for the history API: % ./display.pykey http://server/api/histories/f597429621d6eb2b/contents Collection Members -- #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e name: 1.bed type: file id: cc1c6c1afcb4fd4e f597429621d6eb2b is the encoding of '2' with the default id_secret since this dataset is in history ID 2. cc1c6c1afcb4fd4e is the encoding of 'file.1'. --nate This really confuses me. I'll try to explain why: I have a script that runs two workflows one after the other. The ids in the results of workflow 1 are stored in a database, along with some parameters for workflow 2. Then, I run workflow 2 on workflow 1's results. In this workflow I have a tool that queries the database to get the parameters it needs, so it compares the input ids with those stored previously. If I use this line: $__app__.security.encode_id( 'file.%s' % $input1.id ) It does not match the output ids of workflow 1, so I cannot access the corresponding parameters. But if I use this: $__app__.security.encode_id( '%s' % $input1.id ) the ids match and I get the appropriate database entry. What I understood of it: There must be something wrong somewhere, since I'm clearly manipulating file. free stuff and it works just fine. Those same ids are passed to workflow 2 and it runs properly, on the appropriate datasets. Did I miss anything? Did I do something wrong? L-A Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that? Hi L-A, Pass in as an argument: $__app__.security.encode_id( 'file.%s' % $input1.id ) Where 'input1' is the param name of your input. --nate ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy
Louise-Amélie Schmitt wrote: Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents are all identified by ID, so: http://server/api/libraries/library_id/contents/content_id That content ID can refer to a dataset (file) or folder, but if this was not 'file.id' or 'folder.id', when the framework decoded it, it would just get a numeric ID and wouldn't know to which type it refered. So instead of using just the ID, it uses the encoded form of 'file.id' and 'folder.id'. This was extended to histories even though there isn't a concept of folders in histories. So just encoding the ID is going to give you the encoded HistoryDatasetAssociation id, but that ID won't be the dataset's API id. For example, using the default id_secret in universe_wsgi.ini, if I upload a dataset to a fresh instance of Galaxy, its encoded ID (the encoded value of '1') is: f2db41e1fa331b3e As you can see in the 'display' URL for the dataset: http://server/datasets/f2db41e1fa331b3e/display/ But that ID won't work for the history API: % ./display.pykey http://server/api/histories/f597429621d6eb2b/contents Collection Members -- #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e name: 1.bed type: file id: cc1c6c1afcb4fd4e f597429621d6eb2b is the encoding of '2' with the default id_secret since this dataset is in history ID 2. cc1c6c1afcb4fd4e is the encoding of 'file.1'. --nate This really confuses me. I'll try to explain why: I have a script that runs two workflows one after the other. The ids in the results of workflow 1 are stored in a database, along with some parameters for workflow 2. Then, I run workflow 2 on workflow 1's results. In this workflow I have a tool that queries the database to get the parameters it needs, so it compares the input ids with those stored previously. If I use this line: $__app__.security.encode_id( 'file.%s' % $input1.id ) It does not match the output ids of workflow 1, so I cannot access the corresponding parameters. But if I use this: $__app__.security.encode_id( '%s' % $input1.id ) the ids match and I get the appropriate database entry. What I understood of it: There must be something wrong somewhere, since I'm clearly manipulating file. free stuff and it works just fine. Those same ids are passed to workflow 2 and it runs properly, on the appropriate datasets. Did I miss anything? Did I do something wrong? Ah, no, the workflow API is using the encoded id without 'file.', and specifies the source by using the format: workflow_step_id=type=encoded_id Since the type is provided as a parameter it isn't included in the encoded id. This is more ideal since the encoded id will match what's in the UI, so let me think about how we can do this in the history and library APIs without having ugly URLs. --nate L-A Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that? Hi L-A, Pass in as an argument: $__app__.security.encode_id( 'file.%s' % $input1.id ) Where 'input1' is the param name of your input. --nate ___ 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/ ___ 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/ ___ 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/ ___ 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/
[galaxy-dev] Tools requiring java can't find java
This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ 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/
Re: [galaxy-dev] Tools requiring java can't find java
Yes, your java path is not set, because you are using an non-login shell. Indeed, you should be talking to your sysadmins. George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a From: Chorny, Ilya icho...@illumina.commailto:icho...@illumina.com Date: Tue, 30 Aug 2011 19:23:42 +0300 To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Tools requiring java can't find java This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ 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/
Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy
Le 30/08/2011 18:00, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents are all identified by ID, so: http://server/api/libraries/library_id/contents/content_id That content ID can refer to a dataset (file) or folder, but if this was not 'file.id' or 'folder.id', when the framework decoded it, it would just get a numeric ID and wouldn't know to which type it refered. So instead of using just the ID, it uses the encoded form of 'file.id' and 'folder.id'. This was extended to histories even though there isn't a concept of folders in histories. So just encoding the ID is going to give you the encoded HistoryDatasetAssociation id, but that ID won't be the dataset's API id. For example, using the default id_secret in universe_wsgi.ini, if I upload a dataset to a fresh instance of Galaxy, its encoded ID (the encoded value of '1') is: f2db41e1fa331b3e As you can see in the 'display' URL for the dataset: http://server/datasets/f2db41e1fa331b3e/display/ But that ID won't work for the history API: % ./display.pykey http://server/api/histories/f597429621d6eb2b/contents Collection Members -- #1: /api/histories/f597429621d6eb2b/contents/cc1c6c1afcb4fd4e name: 1.bed type: file id: cc1c6c1afcb4fd4e f597429621d6eb2b is the encoding of '2' with the default id_secret since this dataset is in history ID 2. cc1c6c1afcb4fd4e is the encoding of 'file.1'. --nate This really confuses me. I'll try to explain why: I have a script that runs two workflows one after the other. The ids in the results of workflow 1 are stored in a database, along with some parameters for workflow 2. Then, I run workflow 2 on workflow 1's results. In this workflow I have a tool that queries the database to get the parameters it needs, so it compares the input ids with those stored previously. If I use this line: $__app__.security.encode_id( 'file.%s' % $input1.id ) It does not match the output ids of workflow 1, so I cannot access the corresponding parameters. But if I use this: $__app__.security.encode_id( '%s' % $input1.id ) the ids match and I get the appropriate database entry. What I understood of it: There must be something wrong somewhere, since I'm clearly manipulating file. free stuff and it works just fine. Those same ids are passed to workflow 2 and it runs properly, on the appropriate datasets. Did I miss anything? Did I do something wrong? Ah, no, the workflow API is using the encoded id without 'file.', and specifies the source by using the format: workflow_step_id=type=encoded_id Since the type is provided as a parameter it isn't included in the encoded id. This is more ideal since the encoded id will match what's in the UI, so let me think about how we can do this in the history and library APIs without having ugly URLs. --nate Ah ok, I get it :) Thanks for all the information! Best, L-A L-A Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that? Hi L-A, Pass in as an argument: $__app__.security.encode_id( 'file.%s' % $input1.id ) Where 'input1' is the param name of your input. --nate ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Tools requiring java can't find java
How do I set my path in a non login shell? From: George Marselis [mailto:george.marse...@kaust.edu.sa] Sent: Tuesday, August 30, 2011 9:40 AM To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tools requiring java can't find java Yes, your java path is not set, because you are using an non-login shell. Indeed, you should be talking to your sysadmins. George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a From: Chorny, Ilya icho...@illumina.commailto:icho...@illumina.com Date: Tue, 30 Aug 2011 19:23:42 +0300 To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Tools requiring java can't find java This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ 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/
Re: [galaxy-dev] Tools requiring java can't find java
The following has a bit of advice on that: http://www.admon.org/difference-between-login-shell-and-non-login-shell/ chris On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote: How do I set my path in a non login shell? From: George Marselis [mailto:george.marse...@kaust.edu.sa] Sent: Tuesday, August 30, 2011 9:40 AM To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tools requiring java can't find java Yes, your java path is not set, because you are using an non-login shell. Indeed, you should be talking to your sysadmins. George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a From: Chorny, Ilya icho...@illumina.com Date: Tue, 30 Aug 2011 19:23:42 +0300 To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Tools requiring java can't find java This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.com Website: www.illumina.com ___ 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/ ___ 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/
Re: [galaxy-dev] Tools requiring java can't find java
Gah, wrong link, apologies (the other one is okay, if a bit wonky): http://www.linuxfromscratch.org/blfs/view/cvs/postlfs/profile.html chrus On Aug 30, 2011, at 1:12 PM, Chris Fields wrote: The following has a bit of advice on that: http://www.admon.org/difference-between-login-shell-and-non-login-shell/ chris On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote: How do I set my path in a non login shell? From: George Marselis [mailto:george.marse...@kaust.edu.sa] Sent: Tuesday, August 30, 2011 9:40 AM To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tools requiring java can't find java Yes, your java path is not set, because you are using an non-login shell. Indeed, you should be talking to your sysadmins. George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a From: Chorny, Ilya icho...@illumina.com Date: Tue, 30 Aug 2011 19:23:42 +0300 To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Tools requiring java can't find java This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.com Website: www.illumina.com ___ 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/ ___ 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/
[galaxy-dev] August 30, 2011 Galaxy Development News Brief
August 30, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/News%20Briefs/2011_08_30 Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 949e4f5fa03a What's New ISMB/ECCB, BOSC, and 3DSIG 2011 Slides Recent Publications GalaxyProject.org Wiki Tool Shed Upcoming Events Updated Improved Data Tools Visualization (Trackster) Workflows API Source Quotas Bug Fixes ___ 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/
