GotCloud: RedHat Package - Revision history

Mktrost: moved Pipeline RedHatPackage to GotCloud: RedHat Package

2013-03-18T20:31:24Z

moved Pipeline RedHatPackage to GotCloud: RedHat Package

← Older revision	Revision as of 16:31, 18 March 2013
(No difference)

Terry Gliedt at 16:53, 29 January 2013

2013-01-29T16:53:32Z

← Older revision		Revision as of 12:53, 29 January 2013
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	The ~~BioPipeline~~ software is distributed in several RPM packages.		The GotCloud software is distributed in several RPM packages.
	These can be installed on Fedora, CentOS or Redhat systems.		These can be installed on Fedora, CentOS or Redhat systems.
	It has only been tested on CentOS 6.3, but should run on any recent Redhat-based system.		It has only been tested on CentOS 6.3, but should run on any recent Redhat-based system.

Mktrost at 17:47, 15 November 2012

2012-11-15T17:47:04Z

← Older revision		Revision as of 13:47, 15 November 2012
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	'''Installing RPM Packages'''		'''Installing RPM Packages'''

	Back to parent [~~http://genome.sph.umich.edu/wiki/Pipelines~~]		Back to parent: [[GotCloud]]

	'''<font color='red'>Note - RPMs are not generated at this time</font>'''		'''<font color='red'>Note - RPMs are not generated at this time</font>'''

Terry Gliedt at 13:27, 23 October 2012

2012-10-23T13:27:02Z

← Older revision		Revision as of 09:27, 23 October 2012
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	Back to parent [http://genome.sph.umich.edu/wiki/Pipelines]		Back to parent [http://genome.sph.umich.edu/wiki/Pipelines]

	'''Note - RPMs are not generated at this time'''		'''<font color='red'>Note - RPMs are not generated at this time</font>'''

Terry Gliedt at 13:25, 23 October 2012

2012-10-23T13:25:15Z

← Older revision		Revision as of 09:25, 23 October 2012
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	~~For~~ the ~~moment~~, we are ~~not creating Redhat~~ (~~Fedora~~) ~~RPM~~ packages. ~~When we do~~, ~~they will behave exactly like~~ the ~~Debian~~ packages and ~~their names will~~ be ~~nearly identical~~.		'''Installing RPM Packages'''

			Back to parent [http://genome.sph.umich.edu/wiki/Pipelines]

			'''Note - RPMs are not generated at this time'''


			The BioPipeline software is distributed in several RPM packages.
			These can be installed on Fedora, CentOS or Redhat systems.
			It has only been tested on CentOS 6.3, but should run on any recent Redhat-based system.
			This software should work on any Unix system - only requiring recompilation from the source files.

			The software is distributed in two parts, the ''aligner'' and ''umake''. Each has a package to test the installation. The following naming conventions are used:

			<code>
			biopipe-align_M.m.x86_64.rpm aligner
			biopipe-umake_M.n.x86_64.rpm umake
			biopipe-testalign_M.n.x86_64.rpm
			biopipe-testumake_M.n.x86_64.rpm
			</code>

			where 'M.n' are the normal major-minor version system.
			The package files are available from our public FTP site:

			<code>
			# The easiest way:
			<b>wget ftp://share.sph.umich.edu/biopipe/\*.rpm</b>

			# Another way
			<b>ftp share.sph.umich.edu</b>
			Connected to share.sph.umich.edu.
			220 (vsFTPd 2.3.5)
			Name (share.sph.umich.edu:tpg): <b>anonymous</b>
			230 Login successful.
			Remote system type is UNIX.
			Using binary mode to transfer files.
			ftp> <b>prompt</b>
			Interactive mode off.
			ftp> <b>cd biopipe</b>
			250 Directory successfully changed.
			ftp> <b>mget biopipe*.rpm</b>
			ftp> <b>quit</b>
			221 Goodbye.
			</code>

			Installation requires one to have <b>root access</b> and uses <b>rpm</b> which Redhat users will recognize.
			We recommend you install the first one separately so you can easily
			identify messages about prerequisite files that need to be installed:

			<code>
			<b>sudo rpm -i debs/biopipe-align_*.rpm</b>

			details to come here

			Created symlink '/usr/local/bin/gen_biopipeline.pl' to make running the aligner easier.
			#============================================================
			# 'java' is not installed, do 'sudo yum install java ???'
			#============================================================
			#============================================================
			# 'make' is not installed, do 'sudo yum install make'
			#============================================================
			#============================================================
			# '/usr/local/biopipe/test/align' does not exist so you cannot test this install
			# Install it by doing 'sudo rpm -i biopipe-testalign*.rpm'
			#============================================================
			</code>

			If there were messages about missing packages, install them now

			<code>
			<b>sudo yum install make java-common default-jre ????</b>
			</code>

			Finally, install the other packages. We recommend that at least the first time,
			you install the test packages so you can conveniently test the installation and make sure everything runs smoothly.
			The tests run within a few minutes and are self checking, so unless you see obvious errors,
			you can be reasonably sure everything is set up properly.

			<code>
			<b>sudo rpm -i biopipe-umake_*.rpm</b>

			<b>sudo rpm -i biopipe-test*.rpm</b>
			</code>

			If you installed the test packages, test your installation. You only need to do this once,
			unless you have made signifcant changes to your Unix system.
			Login as a normal user (not as root) and do:

			<code>
			# Test the aligner (fast, about 3 minutes)
			<b>/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign</b>
			rm -rf ~/testalign # If no error

			# Test umake (longer, about 15 minutes)
			<b>/usr/local/biopipe/bin/umake.pl --test ~/testumake</b>
			rm -rf ~/testumake # If no error
			</code>

Terry Gliedt: Created page with 'For the moment, we are not creating Redhat (Fedora) RPM packages. When we do, they will behave exactly like the Debian packages and their names will be nearly identical.'

2012-10-22T20:02:04Z

Created page with 'For the moment, we are not creating Redhat (Fedora) RPM packages. When we do, they will behave exactly like the Debian packages and their names will be nearly identical.'

New page

For the moment, we are not creating Redhat (Fedora) RPM packages. When we do, they will behave exactly like the Debian packages and their names will be nearly identical.