Galaxy on cloud config issues
Hello, Does anybody use the last Galaxy image? I am running Galaxy image on EC2: Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 It looks as those three tools have configuration problems: EBOSS Blast+ meme For all three I am getting a message that looks like that: /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp Is there a way to fix configuration files for those tools? Thank you. Best Regards, Anatoly </pre><P><FONT face="Verdana" color=blue size=1><SPAN style="FONT-SIZE: 8pt; COLOR: blue"> This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. </SPAN></FONT></P>
A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly < Ulyanov_Anatoly@allergan.com> wrote:
Hello,****
** **
Does anybody use the last Galaxy image? I am running Galaxy image on EC2:* ***
** **
Instance ID i-1b2d3773****
Image ID (AMI) ami-118bfc78 ****
** **
It looks as those three tools have configuration problems:****
** **
EBOSS****
Blast+****
meme****
** **
For all three I am getting a message that looks like that:****
** **
/mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found ****
Error invoking command: blastp****
** **
Is there a way to fix configuration files for those tools?****
** **
Thank you.****
** **
Best Regards,****
Anatoly****
** **
This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation.
___________________________________________________________ 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/
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Anatoly, did this method work for you? It is not working for me. ________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Dannon Baker [dannon.baker@gmail.com] Sent: Wednesday, August 07, 2013 8:00 PM To: Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy on cloud config issues A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <Ulyanov_Anatoly@allergan.com<mailto:Ulyanov_Anatoly@allergan.com>> wrote: Hello, Does anybody use the last Galaxy image? I am running Galaxy image on EC2: Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 It looks as those three tools have configuration problems: EBOSS Blast+ meme For all three I am getting a message that looks like that: /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp Is there a way to fix configuration files for those tools? Thank you. Best Regards, Anatoly This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___________________________________________________________ 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/
Ravpreet -- can you provide details as to what's failing for you? If I remember correctly, you had an odd issue where nothing was actually appearing at /mnt, right? This will not be the same issue as the tool volume update. On Thu, Aug 8, 2013 at 4:36 PM, Ravpreet Setia <Ravpreet.Setia@oicr.on.ca>wrote:
Anatoly, did this method work for you? It is not working for me. ------------------------------ *From:* galaxy-dev-bounces@lists.bx.psu.edu [ galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Dannon Baker [ dannon.baker@gmail.com] *Sent:* Wednesday, August 07, 2013 8:00 PM *To:* Ulyanov_Anatoly *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Galaxy on cloud config issues
A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following:
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop
On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly < Ulyanov_Anatoly@allergan.com> wrote:
Hello,****
** **
Does anybody use the last Galaxy image? I am running Galaxy image on EC2: ****
** **
Instance ID i-1b2d3773****
Image ID (AMI) ami-118bfc78 ****
** **
It looks as those three tools have configuration problems:****
** **
EBOSS****
Blast+****
meme****
** **
For all three I am getting a message that looks like that:****
** **
/mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found ****
Error invoking command: blastp****
** **
Is there a way to fix configuration files for those tools?****
** **
Thank you.****
** **
Best Regards,****
Anatoly****
** **
This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation.
___________________________________________________________ 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/
Yeah, nothing happens after SGE gets to the running state. The directory structure of the old ami does not appear in /mnt. The log was posted in the following thread: "Cloudman - When will the symlinks be resolved ?" Additionally, I am not sure what you mean by, "This will not be the same issue as the tool volume update.". Thanks ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Thursday, August 08, 2013 4:40 PM To: Ravpreet Setia Cc: Ulyanov_Anatoly; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy on cloud config issues Ravpreet -- can you provide details as to what's failing for you? If I remember correctly, you had an odd issue where nothing was actually appearing at /mnt, right? This will not be the same issue as the tool volume update. On Thu, Aug 8, 2013 at 4:36 PM, Ravpreet Setia <Ravpreet.Setia@oicr.on.ca<mailto:Ravpreet.Setia@oicr.on.ca>> wrote: Anatoly, did this method work for you? It is not working for me. ________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu>] on behalf of Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: Wednesday, August 07, 2013 8:00 PM To: Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Galaxy on cloud config issues A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <Ulyanov_Anatoly@allergan.com<mailto:Ulyanov_Anatoly@allergan.com>> wrote: Hello, Does anybody use the last Galaxy image? I am running Galaxy image on EC2: Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 It looks as those three tools have configuration problems: EBOSS Blast+ meme For all three I am getting a message that looks like that: /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp Is there a way to fix configuration files for those tools? Thank you. Best Regards, Anatoly This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___________________________________________________________ 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/
On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia <Ravpreet.Setia@oicr.on.ca>wrote:
Yeah, nothing happens after SGE gets to the running state. The directory structure of the old ami does not appear in /mnt. The log was posted in the following thread:
Ahh, ok - I assumed since there was no further reply that the workaround worked for you. I'll take another look at your log, but if you could follow up (on that other thread) with some more details about your cluster that'd be great. Specifically, how you're launching it, if it's an old cluster being relaunched, a share_string-based new cluster, etc. Additionally, I am not sure what you mean by, "This will not be the same
issue as the tool volume update.".
If your volume isn't even mounting, then it has nothing to do with the symlinks referred to by Ulyanov. His volume mounts, it's just not completely functional.
Initially Anatoly and I had the problem with the symlinks and were prescribed the link to launch the old ami as a temporary solution until the latest ami gets fixed. Thus I was curious if Anatoly would experience the same issue as me when launching the older ami this way. Anyways, I'll continue the discussion on the other thread. Thanks! ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Thursday, August 08, 2013 5:08 PM To: Ravpreet Setia Cc: Ulyanov_Anatoly; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy on cloud config issues On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia <Ravpreet.Setia@oicr.on.ca<mailto:Ravpreet.Setia@oicr.on.ca>> wrote: Yeah, nothing happens after SGE gets to the running state. The directory structure of the old ami does not appear in /mnt. The log was posted in the following thread: Ahh, ok - I assumed since there was no further reply that the workaround worked for you. I'll take another look at your log, but if you could follow up (on that other thread) with some more details about your cluster that'd be great. Specifically, how you're launching it, if it's an old cluster being relaunched, a share_string-based new cluster, etc. Additionally, I am not sure what you mean by, "This will not be the same issue as the tool volume update.". If your volume isn't even mounting, then it has nothing to do with the symlinks referred to by Ulyanov. His volume mounts, it's just not completely functional.
Hello Ravpreet, It is not working for me either. I posted a detail reply later. Best Regards, Anatoly From: Ravpreet Setia [mailto:Ravpreet.Setia@oicr.on.ca] Sent: Thursday, August 08, 2013 1:37 PM To: Dannon Baker; Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Galaxy on cloud config issues Anatoly, did this method work for you? It is not working for me. ________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Dannon Baker [dannon.baker@gmail.com] Sent: Wednesday, August 07, 2013 8:00 PM To: Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy on cloud config issues A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <Ulyanov_Anatoly@allergan.com<mailto:Ulyanov_Anatoly@allergan.com>> wrote: Hello, Does anybody use the last Galaxy image? I am running Galaxy image on EC2: Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 It looks as those three tools have configuration problems: EBOSS Blast+ meme For all three I am getting a message that looks like that: /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp Is there a way to fix configuration files for those tools? Thank you. Best Regards, Anatoly This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___________________________________________________________ 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/ </pre><P><FONT face="Verdana" color=blue size=1><SPAN style="FONT-SIZE: 8pt; COLOR: blue"> This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. </SPAN></FONT></P>
Hello Dannon, This bucket did not launch Galaxy properly. Here is the whole Cluster status log: 22:11:22 - Master starting 22:11:23 - Completed initial cluster configuration. This seems to be a new cluster; waiting to configure the type 22:11:27 - SGE prerequisites OK; starting the service 22:11:35 - Configuring SGE... 22:11:45 - Successfully setup SGE; configuring SGE 22:11:46 - Saved file 'persistent_data.yaml' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' 22:11:46 - Saved file 'cm_boot.py' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' 22:11:47 - Saved file 'cm.tar.gz' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' 22:11:47 - Saved file 'EmptyGalaxy.clusterName' to bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' The "Access Galaxy" button on CloudMan Console stays gray and the Services Control panel on Admin Console shows that Galaxy and PostgreSQL are not running. Maybe the log file gives you a clue: 'pd.yaml' not found at paths.py load! Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central' Python version: (2, 6) Image configuration suports: {'apps': ['cloudman', 'galaxy']} [DEBUG] app:54 2013-08-08 22:11:22,729: Initializing app [DEBUG] app:55 2013-08-08 22:11:22,729: Running on 'ec2' type of cloud. [DEBUG] app:72 2013-08-08 22:11:22,729: Getting pd.yaml [DEBUG] ec2:275 2013-08-08 22:11:22,730: No S3 Connection, creating a new one. [DEBUG] ec2:278 2013-08-08 22:11:22,730: Got boto S3 connection. [DEBUG] misc:113 2013-08-08 22:11:22,761: Checking if bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' exists... it does not. [DEBUG] misc:444 2013-08-08 22:11:22,761: Bucket 'cm-bcf1a9a44e022cfe983b8302199ed978' does not exist, did not get remote file 'persistent_data.yaml' ... Thank you. Best Regards, Anatoly From: Dannon Baker [mailto:dannon.baker@gmail.com] Sent: Wednesday, August 07, 2013 5:01 PM To: Ulyanov_Anatoly Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy on cloud config issues A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <Ulyanov_Anatoly@allergan.com<mailto:Ulyanov_Anatoly@allergan.com>> wrote: Hello, Does anybody use the last Galaxy image? I am running Galaxy image on EC2: Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 It looks as those three tools have configuration problems: EBOSS Blast+ meme For all three I am getting a message that looks like that: /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp Is there a way to fix configuration files for those tools? Thank you. Best Regards, Anatoly This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___________________________________________________________ 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/ </pre><P><FONT face="Verdana" color=blue size=1><SPAN style="FONT-SIZE: 8pt; COLOR: blue"> This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. </SPAN></FONT></P>
participants (3)
-
Dannon Baker -
Ravpreet Setia -
Ulyanov_Anatoly