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Question: Are Tools Must Be Installed In Local Machine?
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gravatar for Sachit Adhikari
6.1 years ago by
Sachit Adhikari • 320
Sachit Adhikari • 320 wrote:
Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are those tools must be installed in order to work in Galaxy. For example: I am using Debian machine(Don't have tophat and bowtie installed). Will tophat and bowtie work in my local galaxy? Thanks
alignment bowtie • 795 views
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modified 6.1 years ago by Björn Grüning • 350 • written 6.1 years ago by Sachit Adhikari • 320
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gravatar for Björn Grüning
6.1 years ago by
Björn Grüning • 350
Björn Grüning • 350 wrote:
Hi Sachit, you need to install such tools by yourself, unless you are using some new tools from the toolshed. For example the ncbi-tools or BWA from the toolshed are capable of installing all dependency automatically. In the future the plan is to move all heavy tools to the toolshed with automatic dependency and version handling, afaik. Regards, Bjoern
ADD COMMENT • link written 6.1 years ago by Björn Grüning • 350
I don't think you understood my question very well. Tophat and Bowtie are available by default in Galaxy. Tophat and Bowtie however is not installed in my operating system. Will it still work in Galaxy? On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning <
ADD REPLY • link written 6.1 years ago by Sachit Adhikari • 320
Hi Sachit, Björn answer is correct. The issue is what is a "tool". There are what Galaxy calls "tools". Some of which are installed by default and some of which you can install from the toolshed. There are in many cases just wrappers to third-party tools that need to be installed and available in the environment PATH of the user running Galaxy. Examples of these are TopHat, Bowtie and BWA. Björn mentions in some cases the third-party tool is automatically installed, but this is new and most third-party tools need to be installed manually still. If you are using Debian, thanks to the "Debian Med Team", many tools are already available in the repositories. Both TopHat and Bowtie are. So apt-getting them should do for you. Just remember to configure the .loc files in Galaxy with the location of the index files. This link will be helpful: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Hope this helps, Carlos On Mon, Oct 8, 2012 at 6:48 AM, Sachit Adhikari
ADD REPLY • link written 6.1 years ago by Carlos Borroto • 390
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