Re: [galaxy-dev] Cloudman - Software does not work due to broken symlinks
I am launching instances with the brand new AMI, ami-118bfc78. The symlinks are broken for me. Is there an additional step I need to take after launching the instances? I feel like I am overlooking something. Also, fixing bow tie along with top-hat did not fix the error. I will look into this further. Thanks for any suggestions. From: Enis Afgan mailto:eaf...@emory.edu>> Date: Fri, 12 Jul 2013 18:02:30 +0200 To: Microsoft Office User mailto:ravpreet.se...@oicr.on.ca>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Cloudman - Software does not work due to broken symlinks Is this a migrated cluster or a brand new one? I'm guessing you're using the new AMI? The migration process supposed to have updated those env.sh paths. More to the point, is your tophat job failing due to bowtie not being found? Try adding the path to bowtie executables to tophat's env.sh file as well and see if that fixes the issue. On Fri, Jul 12, 2013 at 5:26 PM, Ravpreet Setia mailto:ravpreet.se...@oicr.on.ca>> wrote: This may be a problem with the latest Galaxy Cloudman AMI. Some tools (tophat is one) are failing to run because they cannot be found. I have noticed that after launching a new instance with the latest AMI, the "//default" sym-links under /mnt/galaxy/tools point to a directory in /mnt/galaxyTools, which does not exist since this new AMI merged galaxyTools and galaxyData. Additionally, even after manually fixing the symlink and the path in the env.sh file (it also references galaxyTools), running tophat would fail, although now, at least, it can find the program. This may be an issue with tophat's XML or python script though, since I fixed Velvet's symlink and env.sh and it worked perfectly. This document explains how the default symlink and env.sh are used by Galaxy: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Thanks for any suggestions. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cloudman - Software does not work due to broken symlinks
Is this a migrated cluster or a brand new one? I'm guessing you're using the new AMI? The migration process supposed to have updated those env.sh paths. More to the point, is your tophat job failing due to bowtie not being found? Try adding the path to bowtie executables to tophat's env.sh file as well and see if that fixes the issue. On Fri, Jul 12, 2013 at 5:26 PM, Ravpreet Setia wrote: > This may be a problem with the latest Galaxy Cloudman AMI. > > Some tools (tophat is one) are failing to run because they cannot be > found. I have noticed that after launching a new instance with the latest > AMI, the "//default" sym-links under /mnt/galaxy/tools > point to a directory in /mnt/galaxyTools, which does not exist since this > new AMI merged galaxyTools and galaxyData. > > Additionally, even after manually fixing the symlink and the path in the > env.sh file (it also references galaxyTools), running tophat would fail, > although now, at least, it can find the program. This may be an issue with > tophat's XML or python script though, since I fixed Velvet's symlink and > env.sh and it worked perfectly. > > This document explains how the default symlink and env.sh are used by > Galaxy: > http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies > > Thanks for any suggestions. > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cloudman - Software does not work due to broken symlinks
This may be a problem with the latest Galaxy Cloudman AMI. Some tools (tophat is one) are failing to run because they cannot be found. I have noticed that after launching a new instance with the latest AMI, the "//default" sym-links under /mnt/galaxy/tools point to a directory in /mnt/galaxyTools, which does not exist since this new AMI merged galaxyTools and galaxyData. Additionally, even after manually fixing the symlink and the path in the env.sh file (it also references galaxyTools), running tophat would fail, although now, at least, it can find the program. This may be an issue with tophat's XML or python script though, since I fixed Velvet's symlink and env.sh and it worked perfectly. This document explains how the default symlink and env.sh are used by Galaxy: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Thanks for any suggestions. ___ 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/
