Adding GATK tools to Galaxy Cloudman
Hi Team, I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham <Iry.Witham@jax.org> wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed.
Thanks,
Iry
Did you solve this Iry? I'm seeing the same "Initializing repository installation failed" error intermediately myself, for instance with package_freetype_2_4 just now - I'm unclear if this was a false alarm or not. I am currently deinstalling/reinstalling things. Peter
Hi Peter,
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham <Iry.Witham@jax.org> wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed.
Thanks,
Iry
Did you solve this Iry?
I'm seeing the same "Initializing repository installation failed" error intermediately myself, for instance with package_freetype_2_4 just now - I'm unclear if this was a false alarm or not. I am currently deinstalling/reinstalling things.
do you see it in the web interface? It's a false positive warning. It never did any harm for me. I think I have filled it as trello issue once, beside many other small usability bugs, but as usual I could not find the card.
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On Mon, Aug 12, 2013 at 12:51 PM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Peter,
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham <Iry.Witham@jax.org> wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed.
Thanks,
Iry
Did you solve this Iry?
I'm seeing the same "Initializing repository installation failed" error intermediately myself, for instance with package_freetype_2_4 just now - I'm unclear if this was a false alarm or not. I am currently deinstalling/reinstalling things.
do you see it in the web interface? It's a false positive warning. It never did any harm for me. I think I have filled it as trello issue once, beside many other small usability bugs, but as usual I could not find the card.
Yes, it pops up in the middle of the web interface - I wasn't sure if it was a real failure or not, so you may be right about it being a false positive. Thanks. Peter
participants (3)
-
Bjoern Gruening -
Iry Witham -
Peter Cock