changing file storage location
Greetings, My name is Ravi Sanka. I have a question regarding Galaxy. Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files. I opened the config file universe_wsgi.ini and did the following: - Removed the '#' mark from '#file_path = database/files' - Changed value of file_path to the absolute path of an accessible, readable/writable location - Saved changes Despite this, the install still stores files in database/files. Is there a step I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again? I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection. Thank you for your time. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -----------------------------------------------
Hi Ravi, Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location. Enis On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:
Greetings,****
** **
My name is Ravi Sanka. I have a question regarding Galaxy.****
****
Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files.****
** **
I opened the config file universe_wsgi.ini and did the following:****
** **
**- **Removed the ‘#’ mark from ‘#file_path = database/files’****
**- **Changed value of file_path to the absolute path of an accessible, readable/writable location****
**- **Saved changes****
** **
Despite this, the install still stores files in database/files. Is there a step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be run again?****
** **
I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection.****
** **
Thank you for your time.****
** **
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
** **
___________________________________________________________ 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:
Hi Enis, No I didn't restart Galaxy after the changes were saved. Is that the process explained in the README.txt (setup.sh & run.sh)? That process was for the first time, so I didn't repeat it after saving the changes. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------- From: Enis Afgan [mailto:eafgan@emory.edu] Sent: Wednesday, June 29, 2011 11:32 AM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] changing file storage location Hi Ravi, Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location. Enis On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org<mailto:rsanka@jcvi.org>> wrote: Greetings, My name is Ravi Sanka. I have a question regarding Galaxy. Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files. I opened the config file universe_wsgi.ini and did the following: - Removed the '#' mark from '#file_path = database/files' - Changed value of file_path to the absolute path of an accessible, readable/writable location - Saved changes Despite this, the install still stores files in database/files. Is there a step I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again? I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection. Thank you for your time. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743<tel:301-795-7743> ----------------------------------------------- ___________________________________________________________ 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/
In order for Galaxy to acknowledge the changes, you'll have to restart Galaxy. I'll double check in the wiki to make sure this is stated somewhere but simply stopping the Galaxy process and starting it back up should reload the config file. If your Galaxy is running the background run: sh run.sh --stop-daemon sh run.sh --daemon If the process is not running in the background, simply stop it (i.e., ctrl + C) Enis On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:
Hi Enis,****
** **
No I didn’t restart Galaxy after the changes were saved. Is that the process explained in the README.txt (setup.sh & run.sh)? That process was for the first time, so I didn’t repeat it after saving the changes.****
** **
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
** **
*From:* Enis Afgan [mailto:eafgan@emory.edu] *Sent:* Wednesday, June 29, 2011 11:32 AM *To:* Sanka, Ravi *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] changing file storage location****
** **
Hi Ravi,****
Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location.****
** **
Enis****
On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:****
Greetings,****
****
My name is Ravi Sanka. I have a question regarding Galaxy.****
****
Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files.****
****
I opened the config file universe_wsgi.ini and did the following:****
****
- Removed the ‘#’ mark from ‘#file_path = database/files’****
- Changed value of file_path to the absolute path of an accessible, readable/writable location****
- Saved changes****
****
Despite this, the install still stores files in database/files. Is there a step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be run again?****
****
I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection.****
****
Thank you for your time.****
****
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
****
___________________________________________________________ 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:
** **
Hello Enis, Thank you. Galaxy is now directing the files to the new storage location. On a related note, I am also planning to switch Galaxy from the default SQLite to an existing MYSQL database. The documentation says to do this, the database_connection field in the config file must be given the proper URL. This is the example it gave: database_connection = postgres:///<db_name><?user=user_name&password=your_pass> Would the same value work if postgres was switched out with mysql? ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------- From: Enis Afgan [mailto:eafgan@emory.edu] Sent: Wednesday, June 29, 2011 12:02 PM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] changing file storage location In order for Galaxy to acknowledge the changes, you'll have to restart Galaxy. I'll double check in the wiki to make sure this is stated somewhere but simply stopping the Galaxy process and starting it back up should reload the config file. If your Galaxy is running the background run: sh run.sh --stop-daemon sh run.sh --daemon If the process is not running in the background, simply stop it (i.e., ctrl + C) Enis On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi <rsanka@jcvi.org<mailto:rsanka@jcvi.org>> wrote: Hi Enis, No I didn't restart Galaxy after the changes were saved. Is that the process explained in the README.txt (setup.sh & run.sh)? That process was for the first time, so I didn't repeat it after saving the changes. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743<tel:301-795-7743> ----------------------------------------------- From: Enis Afgan [mailto:eafgan@emory.edu<mailto:eafgan@emory.edu>] Sent: Wednesday, June 29, 2011 11:32 AM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] changing file storage location Hi Ravi, Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location. Enis On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org<mailto:rsanka@jcvi.org>> wrote: Greetings, My name is Ravi Sanka. I have a question regarding Galaxy. Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files. I opened the config file universe_wsgi.ini and did the following: - Removed the '#' mark from '#file_path = database/files' - Changed value of file_path to the absolute path of an accessible, readable/writable location - Saved changes Despite this, the install still stores files in database/files. Is there a step I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again? I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection. Thank you for your time. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743<tel:301-795-7743> ----------------------------------------------- ___________________________________________________________ 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/
Almost, mysql requires two forward slashes, like so: database_connection = mysql://galaxy:password_here@ <host>/galaxy?unix_socket=/var/run/mysqld/mysqld.sock NTW, unless you are not absolutely set on MySQL, the Galaxy team prefers PostrgeSQL as the backend database. Enis On Wed, Jun 29, 2011 at 4:03 PM, Sanka, Ravi <rsanka@jcvi.org> wrote:
Hello Enis,****
** **
Thank you. Galaxy is now directing the files to the new storage location.* ***
** **
On a related note, I am also planning to switch Galaxy from the default SQLite to an existing MYSQL database. The documentation says to do this, the database_connection field in the config file must be given the proper URL. This is the example it gave:****
** **
database_connection = postgres:///<db_name><?user=user_name&password=your_pass>****
** **
Would the same value work if postgres was switched out with mysql?****
** **
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
** **
*From:* Enis Afgan [mailto:eafgan@emory.edu] *Sent:* Wednesday, June 29, 2011 12:02 PM
*To:* Sanka, Ravi *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] changing file storage location****
** **
In order for Galaxy to acknowledge the changes, you'll have to restart Galaxy. I'll double check in the wiki to make sure this is stated somewhere but simply stopping the Galaxy process and starting it back up should reload the config file. ****
** **
If your Galaxy is running the background run:****
sh run.sh --stop-daemon****
sh run.sh --daemon****
** **
If the process is not running in the background, simply stop it (i.e., ctrl + C)****
** **
Enis****
On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:****
Hi Enis,****
****
No I didn’t restart Galaxy after the changes were saved. Is that the process explained in the README.txt (setup.sh & run.sh)? That process was for the first time, so I didn’t repeat it after saving the changes.****
****
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
****
*From:* Enis Afgan [mailto:eafgan@emory.edu] *Sent:* Wednesday, June 29, 2011 11:32 AM *To:* Sanka, Ravi *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] changing file storage location****
****
Hi Ravi,****
Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location.****
****
Enis****
On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:****
Greetings,****
****
My name is Ravi Sanka. I have a question regarding Galaxy.****
****
Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files.****
****
I opened the config file universe_wsgi.ini and did the following:****
****
- Removed the ‘#’ mark from ‘#file_path = database/files’****
- Changed value of file_path to the absolute path of an accessible, readable/writable location****
- Saved changes****
****
Despite this, the install still stores files in database/files. Is there a step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be run again?****
****
I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection.****
****
Thank you for your time.****
****
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
****
___________________________________________________________ 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:
****
** **
Yes, I saw in the documentation that PostrgeSQL is preferred. For the time being, however, I only have access to MYSQL. I noticed in your example URL, there is no spot for username, only password, host, and socket. Does Galaxy not require a username for connecting to a MYSQL database? ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------- From: Enis Afgan [mailto:eafgan@emory.edu] Sent: Wednesday, June 29, 2011 5:06 PM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] changing file storage location Almost, mysql requires two forward slashes, like so: database_connection = mysql://galaxy:password_here@<host>/galaxy?unix_socket=/var/run/mysqld/mysqld.sock NTW, unless you are not absolutely set on MySQL, the Galaxy team prefers PostrgeSQL as the backend database. Enis On Wed, Jun 29, 2011 at 4:03 PM, Sanka, Ravi <rsanka@jcvi.org<mailto:rsanka@jcvi.org>> wrote: Hello Enis, Thank you. Galaxy is now directing the files to the new storage location. On a related note, I am also planning to switch Galaxy from the default SQLite to an existing MYSQL database. The documentation says to do this, the database_connection field in the config file must be given the proper URL. This is the example it gave: database_connection = postgres:///<db_name><?user=user_name&password=your_pass> Would the same value work if postgres was switched out with mysql? ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743<tel:301-795-7743> ----------------------------------------------- From: Enis Afgan [mailto:eafgan@emory.edu<mailto:eafgan@emory.edu>] Sent: Wednesday, June 29, 2011 12:02 PM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] changing file storage location In order for Galaxy to acknowledge the changes, you'll have to restart Galaxy. I'll double check in the wiki to make sure this is stated somewhere but simply stopping the Galaxy process and starting it back up should reload the config file. If your Galaxy is running the background run: sh run.sh --stop-daemon sh run.sh --daemon If the process is not running in the background, simply stop it (i.e., ctrl + C) Enis On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi <rsanka@jcvi.org<mailto:rsanka@jcvi.org>> wrote: Hi Enis, No I didn't restart Galaxy after the changes were saved. Is that the process explained in the README.txt (setup.sh & run.sh)? That process was for the first time, so I didn't repeat it after saving the changes. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743<tel:301-795-7743> ----------------------------------------------- From: Enis Afgan [mailto:eafgan@emory.edu<mailto:eafgan@emory.edu>] Sent: Wednesday, June 29, 2011 11:32 AM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] changing file storage location Hi Ravi, Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location. Enis On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org<mailto:rsanka@jcvi.org>> wrote: Greetings, My name is Ravi Sanka. I have a question regarding Galaxy. Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files. I opened the config file universe_wsgi.ini and did the following: - Removed the '#' mark from '#file_path = database/files' - Changed value of file_path to the absolute path of an accessible, readable/writable location - Saved changes Despite this, the install still stores files in database/files. Is there a step I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again? I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection. Thank you for your time. ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743<tel:301-795-7743> ----------------------------------------------- ___________________________________________________________ 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/
In the string, I assumed 'galaxy' to be the username for accessing the database. The string is standard SQLalchemy connection string: http://www.sqlalchemy.org/docs/core/engines.html#engine-creation-api On Wed, Jun 29, 2011 at 5:11 PM, Sanka, Ravi <rsanka@jcvi.org> wrote:
Yes, I saw in the documentation that PostrgeSQL is preferred. For the time being, however, I only have access to MYSQL.****
** **
I noticed in your example URL, there is no spot for username, only password, host, and socket. Does Galaxy not require a username for connecting to a MYSQL database?****
** **
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
** **
*From:* Enis Afgan [mailto:eafgan@emory.edu] *Sent:* Wednesday, June 29, 2011 5:06 PM
*To:* Sanka, Ravi *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] changing file storage location****
** **
Almost, mysql requires two forward slashes, like so:****
database_connection = mysql://galaxy:password_here@ <host>/galaxy?unix_socket=/var/run/mysqld/mysqld.sock****
** **
NTW, unless you are not absolutely set on MySQL, the Galaxy team prefers PostrgeSQL as the backend database. ****
** **
Enis****
** **
On Wed, Jun 29, 2011 at 4:03 PM, Sanka, Ravi <rsanka@jcvi.org> wrote:****
Hello Enis,****
****
Thank you. Galaxy is now directing the files to the new storage location.* ***
****
On a related note, I am also planning to switch Galaxy from the default SQLite to an existing MYSQL database. The documentation says to do this, the database_connection field in the config file must be given the proper URL. This is the example it gave:****
****
database_connection = postgres:///<db_name><?user=user_name&password=your_pass>****
****
Would the same value work if postgres was switched out with mysql?****
****
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
****
*From:* Enis Afgan [mailto:eafgan@emory.edu] *Sent:* Wednesday, June 29, 2011 12:02 PM****
*To:* Sanka, Ravi *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] changing file storage location****
****
In order for Galaxy to acknowledge the changes, you'll have to restart Galaxy. I'll double check in the wiki to make sure this is stated somewhere but simply stopping the Galaxy process and starting it back up should reload the config file. ****
****
If your Galaxy is running the background run:****
sh run.sh --stop-daemon****
sh run.sh --daemon****
****
If the process is not running in the background, simply stop it (i.e., ctrl + C)****
****
Enis****
On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:****
Hi Enis,****
****
No I didn’t restart Galaxy after the changes were saved. Is that the process explained in the README.txt (setup.sh & run.sh)? That process was for the first time, so I didn’t repeat it after saving the changes.****
****
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
****
*From:* Enis Afgan [mailto:eafgan@emory.edu] *Sent:* Wednesday, June 29, 2011 11:32 AM *To:* Sanka, Ravi *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] changing file storage location****
****
Hi Ravi,****
Just a quick check - did you restart Galaxy after saving the changes? What you did should direct any new files to the specified location.****
****
Enis****
On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi <rsanka@jcvi.org> wrote:****
Greetings,****
****
My name is Ravi Sanka. I have a question regarding Galaxy.****
****
Recently, I had a local installation set up and am now trying to change the location where the install stores imported and created files.****
****
I opened the config file universe_wsgi.ini and did the following:****
****
- Removed the ‘#’ mark from ‘#file_path = database/files’****
- Changed value of file_path to the absolute path of an accessible, readable/writable location****
- Saved changes****
****
Despite this, the install still stores files in database/files. Is there a step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be run again?****
****
I also intend to change the database from the SQLite default to an existing database, so I assume the steps to change the file_path also apply to database_connection.****
****
Thank you for your time.****
****
-----------------------------------------------****
Ravi Sanka****
ICS - Bioinformatics Engineer****
J. Craig Venter Institute****
301-795-7743****
-----------------------------------------------****
****
___________________________________________________________ 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:
****
****
** **
participants (2)
-
Enis Afgan -
Sanka, Ravi