User: Marc

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Marc30
Reputation:
30
Status:
New User
Location:
United Kingdom
Last seen:
2 years, 3 months ago
Joined:
2 years, 7 months ago
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Posts by Marc

<prev • 45 results • page 1 of 5 • next >
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if I update my local galaxy instance, will all the tools I installed and data I imported be gone ?
... Hi all,  if I update my local galaxy instance to a newer version using git, will all the tools I installed and data I imported be gone? Cause I vaguely remember I tried once before and end up reinstall and reconfigure everything. Many thanks ...
local galaxy galaxy update written 2.3 years ago by Marc30 • updated 2.3 years ago by Bjoern Gruening4.8k
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Cloud service choosing
... Hi all,  I've seen some of the implementations to make galaxy more useful and scalable such as cloudman and globus genomics, I wonder why they all choose amazon over microsoft azure cloud.  Does anyone know? Is there any paper that addressed this problem before?  Many thanks ...
cloudman galaxy customizing galaxy instance written 2.3 years ago by Marc30 • updated 2.3 years ago by Martin Čech ♦♦ 4.2k
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Comment: C: workflow running in cluster
... I understand the general idea. It's just I've been reading https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Is DRM the scheduler? Or is it configured in the galaxy.ini? What's confusing me is that how to configure this.  ...
written 2.5 years ago by Marc30
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workflow running in cluster
... Hi all, if i have a workflow of five steps, and i run this workflow on a cluster of 4 nodes, how does it actually work? And if i want to run this workflow for 3 different pairs of data, how does the cluster work in this case?  Many thanks ...
cluster galaxy parrallel workflow azure written 2.5 years ago by Marc30 • updated 2.5 years ago by Bjoern Gruening4.8k
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Comment: C: GATK2 tools installation
...   Yeah I did Install the latest one. So how should I fix it? Looking forward to your reply. Also, do you happen to know the answer to my other question? And when you install gatk2 from the toolshed, other than click install, is there anything else that needs to be configured? Many thanks ...
written 2.5 years ago by Marc30
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Unable to get information from the Tool Shed
... Hi all,  what should i do if the tools i want to install get stuck at cloning step?  I'm trying to install gatk2, and it just won't succeed and there is the blue question mark on the left of the name( Unable to get information from the Tool Shed), how can i fix this? Thanks ...
galaxy azure local instance written 2.5 years ago by Marc30
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Comment: C: Memory requirement? Picard missing tool dependencies
... Hi Jelle, thanks. By the way, do you know that if there is a problem in the gatk2 installation on local galaxy now? cause the installation just stuck at the status of cloning. And at the manage installed tool shed dependencies, the status is Unable to get information from the Tool Shed ...
written 2.5 years ago by Marc30
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GATK2 tools installation
... Hi all,  Why the installation of gatk2 stuck at the status of cloning? I've done this before and it worked fine.  Another question is that the GATK2_PATH(type: set_environment), do I need do any configuration or anything at all about this? Because the GATK2 tools didn't work before due to unable t ...
local galaxy gatk written 2.5 years ago by Marc30
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Comment: C: Memory requirement? Picard missing tool dependencies
... Thanks, but I searched in the tool shed and found three picard available, and all of them has the same missing tool dependencies problem after I installed them.  Another matter is that is it true that the galaxy won't be able take advantage of a multi-core system, and only able to scale by using mu ...
written 2.5 years ago by Marc30
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Problem with can't allocate memory
... Hi all,  After Map with BWA-MEM run successfully, it provides the following message "Generating BWA index with is algorithm [bwa_index] Pack FASTA... 45.22 sec [bwa_index] Construct BWT for the packed sequence... [bwt_pac2bwt] Failed to allocate 6274322529 bytes at bwtindex.c line 81: Cannot alloca ...
galaxy virtual machine written 2.5 years ago by Marc30

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