Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the basic question.
I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers?
Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy?
Thank you!
Ray
Dear all,
I have gotten a bit further and was able to install the Data Managers this time. Previously, I was having problems accessing the ToolShed web site and some Python errors in the log file, but fine ... sort of (I get some intermittent errors accessing the Tool Shed site; maybe it's a problem on my side).
However, with the FASTA fetch tool installed from the Galaxy Main Tool Shed, I selected "Local Data" from the Administrator panel. Under "Run Data Manager Tools", I now have "Bowtie index", "Reference Genome", etc. When I click on any of the options under "Run Data Manager Tools", though, I get a blank page. I mean, I get a user-level menu on the left, history on the right, a menu along the top. But the center is blank. Is there something else I need to do?
If I go to "View Data Manager Jobs", "Reference Genome", though, I get a message that says there are "There are no jobs for this data manager.".
If possible, I would like to upload FASTA files myself to our local Galaxy instance. For reasons which I'm still working on (and which is unrelated to Galaxy), download times are very long. Since I have the FASTA file already, it might be easier to upload one myself; but if that's not something Data Managers can do, I guess I can just start the download and set it aside...
Thank you!
Ray
On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan rwan.work@gmail.com wrote:
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the basic question.
I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers?
Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy?
Thank you!
Ray
Hi Ray
If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to
~/tool-data/bowtie2_indices.loc ~/tool-data/bowtie_indices.loc
This way you prevent duplication of your reference data
Regards, Hans-Rudolf
Dear all,
I have gotten a bit further and was able to install the Data Managers this time. Previously, I was having problems accessing the ToolShed web site and some Python errors in the log file, but fine ... sort of (I get some intermittent errors accessing the Tool Shed site; maybe it's a problem on my side).
However, with the FASTA fetch tool installed from the Galaxy Main Tool Shed, I selected "Local Data" from the Administrator panel. Under "Run Data Manager Tools", I now have "Bowtie index", "Reference Genome", etc. When I click on any of the options under "Run Data Manager Tools", though, I get a blank page. I mean, I get a user-level menu on the left, history on the right, a menu along the top. But the center is blank. Is there something else I need to do?
If I go to "View Data Manager Jobs", "Reference Genome", though, I get a message that says there are "There are no jobs for this data manager.".
If possible, I would like to upload FASTA files myself to our local Galaxy instance. For reasons which I'm still working on (and which is unrelated to Galaxy), download times are very long. Since I have the FASTA file already, it might be easier to upload one myself; but if that's not something Data Managers can do, I guess I can just start the download and set it aside...
Thank you!
Ray
On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan rwan.work@gmail.com wrote:
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the basic question.
I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers?
Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy?
Thank you!
Ray
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Hans-Rudolf,
Thank you for getting back to me!
I did take a peak at those files and they seem self-explanatory. I think I can do that. However, I was worried about the message at the top of:
https://wiki.galaxyproject.org/Admin/DataPreparation
It seemed the method written on that page has now been superseded by Data Managers? I was worried editing *.loc files directly with an editor would break a database and cause more headaches for me. Is that not the case or perhaps I can get away with doing it just for the FASTA files but should still use Data Managers for index generation?
Thank you!
Ray
On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Ray
If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to
~/tool-data/bowtie2_indices.loc ~/tool-data/bowtie_indices.loc
This way you prevent duplication of your reference data
Regards, Hans-Rudolf
Dear all,
I have gotten a bit further and was able to install the Data Managers this time. Previously, I was having problems accessing the ToolShed web site and some Python errors in the log file, but fine ... sort of (I get some intermittent errors accessing the Tool Shed site; maybe it's a problem on my side).
However, with the FASTA fetch tool installed from the Galaxy Main Tool Shed, I selected "Local Data" from the Administrator panel. Under "Run Data Manager Tools", I now have "Bowtie index", "Reference Genome", etc. When I click on any of the options under "Run Data Manager Tools", though, I get a blank page. I mean, I get a user-level menu on the left, history on the right, a menu along the top. But the center is blank. Is there something else I need to do?
If I go to "View Data Manager Jobs", "Reference Genome", though, I get a message that says there are "There are no jobs for this data manager.".
If possible, I would like to upload FASTA files myself to our local Galaxy instance. For reasons which I'm still working on (and which is unrelated to Galaxy), download times are very long. Since I have the FASTA file already, it might be easier to upload one myself; but if that's not something Data Managers can do, I guess I can just start the download and set it aside...
Thank you!
Ray
On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan rwan.work@gmail.com wrote:
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the basic question.
I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers?
Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy?
Thank you!
Ray
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Ray
Well, I guess, you can call me 'old-fashioned' ;)
we still solely rely on manually editing the '*loc' files. The main reason we do that: Most of our reference data is first prepared (by others) for people using it on the command line, and only in a second step we make it available via Galaxy.
Hans-Rudolf
On 02/18/2016 09:00 AM, Raymond Wan wrote:
Hi Hans-Rudolf,
Thank you for getting back to me!
I did take a peak at those files and they seem self-explanatory. I think I can do that. However, I was worried about the message at the top of:
https://wiki.galaxyproject.org/Admin/DataPreparation
It seemed the method written on that page has now been superseded by Data Managers? I was worried editing *.loc files directly with an editor would break a database and cause more headaches for me. Is that not the case or perhaps I can get away with doing it just for the FASTA files but should still use Data Managers for index generation?
Thank you!
Ray
On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Ray
If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to
~/tool-data/bowtie2_indices.loc ~/tool-data/bowtie_indices.loc
This way you prevent duplication of your reference data
Regards, Hans-Rudolf
Dear all,
I have gotten a bit further and was able to install the Data Managers this time. Previously, I was having problems accessing the ToolShed web site and some Python errors in the log file, but fine ... sort of (I get some intermittent errors accessing the Tool Shed site; maybe it's a problem on my side).
However, with the FASTA fetch tool installed from the Galaxy Main Tool Shed, I selected "Local Data" from the Administrator panel. Under "Run Data Manager Tools", I now have "Bowtie index", "Reference Genome", etc. When I click on any of the options under "Run Data Manager Tools", though, I get a blank page. I mean, I get a user-level menu on the left, history on the right, a menu along the top. But the center is blank. Is there something else I need to do?
If I go to "View Data Manager Jobs", "Reference Genome", though, I get a message that says there are "There are no jobs for this data manager.".
If possible, I would like to upload FASTA files myself to our local Galaxy instance. For reasons which I'm still working on (and which is unrelated to Galaxy), download times are very long. Since I have the FASTA file already, it might be easier to upload one myself; but if that's not something Data Managers can do, I guess I can just start the download and set it aside...
Thank you!
Ray
On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan rwan.work@gmail.com wrote:
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the basic question.
I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers?
Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy?
Thank you!
Ray
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Hans-Rudolf,
Actually, I'm also feeling a little "old-fashioned" myself and would prefer to edit .loc files, especially given the amount of documentation out there. I know Data Managers are a next step up, but I don't think I'm smart enough to figure out why I was getting a blank page -- perhaps a problem for another day (that I might ignore unless it bothers users :-) ).
By the way, I just got it working -- thank you for your help!
Ray
On Thu, Feb 18, 2016 at 4:10 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Ray
Well, I guess, you can call me 'old-fashioned' ;)
we still solely rely on manually editing the '*loc' files. The main reason we do that: Most of our reference data is first prepared (by others) for people using it on the command line, and only in a second step we make it available via Galaxy.
Hans-Rudolf
On 02/18/2016 09:00 AM, Raymond Wan wrote:
Hi Hans-Rudolf,
Thank you for getting back to me!
I did take a peak at those files and they seem self-explanatory. I think I can do that. However, I was worried about the message at the top of:
https://wiki.galaxyproject.org/Admin/DataPreparation
It seemed the method written on that page has now been superseded by Data Managers? I was worried editing *.loc files directly with an editor would break a database and cause more headaches for me. Is that not the case or perhaps I can get away with doing it just for the FASTA files but should still use Data Managers for index generation?
Thank you!
Ray
On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Ray
If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to
~/tool-data/bowtie2_indices.loc ~/tool-data/bowtie_indices.loc
This way you prevent duplication of your reference data
Regards, Hans-Rudolf
Hi Ray
Data Managers are designed to co-exist with manually editing the .loc files. So don't worry, edit away.
Peter
On 18 February 2016 at 10:00, Raymond Wan rwan.work@gmail.com wrote:
Hi Hans-Rudolf,
Thank you for getting back to me!
I did take a peak at those files and they seem self-explanatory. I think I can do that. However, I was worried about the message at the top of:
https://wiki.galaxyproject.org/Admin/DataPreparation
It seemed the method written on that page has now been superseded by Data Managers? I was worried editing *.loc files directly with an editor would break a database and cause more headaches for me. Is that not the case or perhaps I can get away with doing it just for the FASTA files but should still use Data Managers for index generation?
Thank you!
Ray
On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Ray
If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to
~/tool-data/bowtie2_indices.loc ~/tool-data/bowtie_indices.loc
This way you prevent duplication of your reference data
Regards, Hans-Rudolf
Dear all,
I have gotten a bit further and was able to install the Data Managers this time. Previously, I was having problems accessing the ToolShed web site and some Python errors in the log file, but fine ... sort of (I get some intermittent errors accessing the Tool Shed site; maybe it's a problem on my side).
However, with the FASTA fetch tool installed from the Galaxy Main Tool Shed, I selected "Local Data" from the Administrator panel. Under "Run Data Manager Tools", I now have "Bowtie index", "Reference Genome", etc. When I click on any of the options under "Run Data Manager Tools", though, I get a blank page. I mean, I get a user-level menu on the left, history on the right, a menu along the top. But the center is blank. Is there something else I need to do?
If I go to "View Data Manager Jobs", "Reference Genome", though, I get a message that says there are "There are no jobs for this data manager.".
If possible, I would like to upload FASTA files myself to our local Galaxy instance. For reasons which I'm still working on (and which is unrelated to Galaxy), download times are very long. Since I have the FASTA file already, it might be easier to upload one myself; but if that's not something Data Managers can do, I guess I can just start the download and set it aside...
Thank you!
Ray
On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan rwan.work@gmail.com
wrote:
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the basic question.
I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers?
Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy?
Thank you!
Ray
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: https://lists.galaxyproject.org/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Peter,
On Thu, Feb 18, 2016 at 4:13 PM, Peter van Heusden pvh@sanbi.ac.za wrote:
Hi Ray
Data Managers are designed to co-exist with manually editing the .loc files. So don't worry, edit away.
Thank you for the clarification! That made me feel better and I pressed ahead and just got it working.
When I first read that Data Managers involved tables, I had this sudden fear that it meant the Postgres database and a mistake will somehow break it. I guess the tables refer to the various .loc text files?
Perhaps when I have the luxury of time, I can try to figure out why the Data Managers weren't working out for me (and also why transferring data from UCSC can take hours or more from our Galaxy instance's network). For now, I'll stick with what works so that the users are happy... :-)
Thank you for your help!
Ray
galaxy-dev@lists.galaxyproject.org
-
Hans-Rudolf Hotz -
Peter van Heusden -
Raymond Wan