I have been asked by a research fellow to setup a local instance of Galaxy. In addition, he would like the latest versions of packages like bowtie, cufflinks, tophat, etc to be installed and available through that instance. Being a newbie to Galaxy, and just a systems administrator responsible for building this environment, I am unsure how exactly to go about doing this. I have an instance running, and worked my way through the fastx-toolkit installation/update but I cannot seem to find a similar how-to for the other packages. Could someone point me in the right direction please? Thank you in advance Michael Weiner UNIX Systems Administrator Lerner Research Institute Cleveland Clinic =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Michael, (I'm CCing galaxy-dev because this has to do with a local installation, not our public server.) There is a wiki page discussing how to install several of the NGS tools, including Bowtie: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup . Note that this page is slightly out-of-date regarding working with the loc files. We have introduced data tables since the page was written and it hasn't yet been updated. There is a basic page on data tables: https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables. TopHat and Cufflinks are not detailed on that page, but the process should be very similar to Bowtie. Let us know if you have further questions. Regards, Kelly On Dec 16, 2010, at 4:12 PM, Weiner, Michael wrote:
I have been asked by a research fellow to setup a local instance of Galaxy. In addition, he would like the latest versions of packages like bowtie, cufflinks, tophat, etc to be installed and available through that instance. Being a newbie to Galaxy, and just a systems administrator responsible for building this environment, I am unsure how exactly to go about doing this.
I have an instance running, and worked my way through the fastx- toolkit installation/update but I cannot seem to find a similar how-to for the other packages. Could someone point me in the right direction please?
Thank you in advance Michael Weiner UNIX Systems Administrator Lerner Research Institute Cleveland Clinic
===================================
P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Thank you Kelly, I will take a look and work my way through that documentation. I appreciate the speedy reply. Not sure why I couldn't find that myself :( Regards Michael -----Original Message----- From: Kelly Vincent [mailto:kpvincent@bx.psu.edu] Sent: Thursday, December 16, 2010 4:31 PM To: Weiner, Michael Cc: galaxy-user@bx.psu.edu; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-user] Setting up a local Galaxy instance Michael, (I'm CCing galaxy-dev because this has to do with a local installation, not our public server.) There is a wiki page discussing how to install several of the NGS tools, including Bowtie: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup . Note that this page is slightly out-of-date regarding working with the loc files. We have introduced data tables since the page was written and it hasn't yet been updated. There is a basic page on data tables: https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables. TopHat and Cufflinks are not detailed on that page, but the process should be very similar to Bowtie. Let us know if you have further questions. Regards, Kelly On Dec 16, 2010, at 4:12 PM, Weiner, Michael wrote:
I have been asked by a research fellow to setup a local instance of Galaxy. In addition, he would like the latest versions of packages like bowtie, cufflinks, tophat, etc to be installed and available through that instance. Being a newbie to Galaxy, and just a systems administrator responsible for building this environment, I am unsure how exactly to go about doing this.
I have an instance running, and worked my way through the fastx- toolkit installation/update but I cannot seem to find a similar how-to for the other packages. Could someone point me in the right direction please?
Thank you in advance Michael Weiner UNIX Systems Administrator Lerner Research Institute Cleveland Clinic
===================================
P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
=================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Kelly Vincent -
Weiner, Michael