Installation and Configuration of FusionSeq - Revision history

Asboner: /* (versions 0.7.0 and later) */

2012-02-09T18:01:49Z

(versions 0.7.0 and later)

← Older revision		Revision as of 18:01, 9 February 2012
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	This procedure installs all core and optional programs into bin/ and the libraries in lib/. Moreover, a configuration file .fusionseqrc is copied in your home directory. This is a text file including the configuration information as KEY=VALUE. The user needs to edit this file in a similar way as the previous versions. '''IMPORTANT''': the location of this file must be assigned to FUSIONSEQ_CONFPATH, e.g.:		This procedure installs all core and optional programs into bin/ and the libraries in lib/. Moreover, a configuration file .fusionseqrc is copied in your home directory. This is a text file including the configuration information as KEY=VALUE. The user needs to edit this file in a similar way as the previous versions. '''IMPORTANT''': the location of this file must be assigned to FUSIONSEQ_CONFPATH, e.g.:
	$ export ~~FUSIONSEQ_PATH~~=/path/2/home/.fusionseqrc		$ export FUSIONSEQ_CONFPATH=/path/2/home/.fusionseqrc

	Here after an example of the configuration file.		Here after an example of the configuration file.

Asboner: /* (versions 0.7.0 and later) */

2012-01-11T11:42:12Z

(versions 0.7.0 and later)

← Older revision		Revision as of 11:42, 11 January 2012
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	RIBOSOMAL_DIR="/path/to/ribosomal/Dir"		RIBOSOMAL_DIR="/path/to/ribosomal/Dir"
	RIBOSOMAL_FILENAME="ribosomal.2bit"		RIBOSOMAL_FILENAME="ribosomal.2bit"
			# Used for gfrRibosomalFilter
			MAX_FRACTION_HOMOLOGOUS=0.05
			MAX_OVERLAP_ALLOWED=0.75

			# Used for gfr2bpJunctions
			MAX_NUMBER_OF_JUNCTION_PER_FILE=2000000

	// ----------------------- This section is optional: visualization tools -------------------------		// ----------------------- This section is optional: visualization tools -------------------------

Asboner: /* (versions 0.7.0 and later) */

2011-06-07T17:01:35Z

(versions 0.7.0 and later)

@@ Line 95: / Line 95: @@
 $ ln -s /path/to/root/lib/* .
 </pre>
 =====(versions up to 0.6.1)=====

Asboner: /* (versions 0.7.0 and later) */

2011-05-17T18:48:25Z

(versions 0.7.0 and later)

← Older revision		Revision as of 18:48, 17 May 2011
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	Please refer to [[#versions 0.6.1\|version 0.6.1]] for instructions of the stable version.		Please refer to [[#versions 0.6.1\|version 0.6.1]] for instructions of the stable version.

	====(versions 0.7.0 and later) ====		=====(versions 0.7.0 and later) =====
	Starting from version 0.7.0 (alpha), libbios and libmrf need to be installed, in this order. Typically, one would run:		Starting from version 0.7.0 (alpha), libbios and libmrf need to be installed, in this order. Typically, one would run:
	<pre>		<pre>

Asboner: /* Installing and configuring ROOT */

2011-05-17T18:48:02Z

Installing and configuring ROOT

← Older revision		Revision as of 18:48, 17 May 2011
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	To install [http://root.cern.ch/drupal/ ROOT], please follow the instructions on the website. You may also include GSL library when compiling, but it is not a requirement. '''NOTE''': for Ubuntu users, the detailed instructions to install [http://root.cern.ch/drupal/ ROOT] can be found [http://cometpeak.com/2011/05/building-and-installing-root-on-ubuntu-11-04-x86_64/ here].		To install [http://root.cern.ch/drupal/ ROOT], please follow the instructions on the website. You may also include GSL library when compiling, but it is not a requirement. '''NOTE''': for Ubuntu users, the detailed instructions to install [http://root.cern.ch/drupal/ ROOT] can be found [http://cometpeak.com/2011/05/building-and-installing-root-on-ubuntu-11-04-x86_64/ here].

	=====(~~version~~ 0.7.0 and later)=====		=====(versions 0.7.0 and later)=====
	If ROOT is installed in the default folder, it will generate a subfolder 'root' both for the include and lib files. In the case of a non-standard location for [http://root.cern.ch/drupal/ ROOT], however, this doesn't occur. Hence, a similar approach as above can be adopted to properly link [http://root.cern.ch/drupal/ ROOT] files for FusionSeq.		If ROOT is installed in the default folder, it will generate a subfolder 'root' both for the include and lib files. In the case of a non-standard location for [http://root.cern.ch/drupal/ ROOT], however, this doesn't occur. Hence, a similar approach as above can be adopted to properly link [http://root.cern.ch/drupal/ ROOT] files for FusionSeq.
	<pre>		<pre>
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	</pre>		</pre>

	=====(~~version~~ up to 0.6.1)=====		=====(versions up to 0.6.1)=====
	Once ROOT is installed, a few variables need to be defined in order to properly use this library with FusionSeq.		Once ROOT is installed, a few variables need to be defined in order to properly use this library with FusionSeq.
	<pre>		<pre>

Asboner: /* (versions up to 0.6.1) */

2011-05-17T18:47:39Z

(versions up to 0.6.1)

← Older revision		Revision as of 18:47, 17 May 2011
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	</pre>		</pre>

	====(versions up to 0.6.1)====		=====(versions up to 0.6.1)=====
	To install [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] a few variables need to be set before compiling the library. Here is an example of the procedure on a bash shell:		To install [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] a few variables need to be set before compiling the library. Here is an example of the procedure on a bash shell:
	<pre>		<pre>

Asboner: /* (versions 0.7.0 and later) -- coming soon */

2011-05-17T18:47:26Z

(versions 0.7.0 and later) -- coming soon

← Older revision		Revision as of 18:47, 17 May 2011
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	Please refer to [[#(versions up to 0.6.1)\|version 0.6.1]] for instruction of the stable version.		Please refer to [[#(versions up to 0.6.1)\|version 0.6.1]] for instruction of the stable version.

	====(versions 0.7.0 and later) ~~-- coming soon~~====		=====(versions 0.7.0 and later)=====
	Once the required packages are properly installed, to install FusionSeq is sufficient to run:		Once the required packages are properly installed, to install FusionSeq is sufficient to run:
	<pre>		<pre>
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	'''NB:''' use '''absolute''' paths in .fusionseqrc, i.e. avoid using environmental variables such as $HOME, etc.		'''NB:''' use '''absolute''' paths in .fusionseqrc, i.e. avoid using environmental variables such as $HOME, etc.


	====(versions up to 0.6.1) ====		====(versions up to 0.6.1) ====

Asboner: /* Installing and configuring ROOT */

2011-05-17T18:46:57Z

Installing and configuring ROOT

← Older revision		Revision as of 18:46, 17 May 2011
Line 83:		Line 83:

	==Installing and configuring ROOT==		==Installing and configuring ROOT==
	To install [http://root.cern.ch/drupal/ ROOT], please follow the instructions on the website. You may also include GSL library when compiling, but it is not a requirement. '''NOTE''': for Ubuntu users, the detailed instructions to install ROOT can be found [http://cometpeak.com/2011/05/building-and-installing-root-on-ubuntu-11-04-x86_64/ here].		To install [http://root.cern.ch/drupal/ ROOT], please follow the instructions on the website. You may also include GSL library when compiling, but it is not a requirement. '''NOTE''': for Ubuntu users, the detailed instructions to install [http://root.cern.ch/drupal/ ROOT] can be found [http://cometpeak.com/2011/05/building-and-installing-root-on-ubuntu-11-04-x86_64/ here].

	=====version up to 0.6.1=====		=====(version 0.7.0 and later)=====
			If ROOT is installed in the default folder, it will generate a subfolder 'root' both for the include and lib files. In the case of a non-standard location for [http://root.cern.ch/drupal/ ROOT], however, this doesn't occur. Hence, a similar approach as above can be adopted to properly link [http://root.cern.ch/drupal/ ROOT] files for FusionSeq.
			<pre>
			$ mkdir ~/fusionseq/include/root
			$ cd ~/fusionseq/include/root
			$ ln -s /path/to/root/include/* .
			$ mkdir ~/fusionseq/lib/root
			$ cd ~/fusionseq/lib/root
			$ ln -s /path/to/root/lib/* .
			</pre>

			=====(version up to 0.6.1)=====
	Once ROOT is installed, a few variables need to be defined in order to properly use this library with FusionSeq.		Once ROOT is installed, a few variables need to be defined in order to properly use this library with FusionSeq.
	<pre>		<pre>

Asboner: /* (versions 0.7.0 and later) */

2011-05-17T18:44:35Z

(versions 0.7.0 and later)

@@ Line 66: / Line 66: @@
 $ export CPPFLAGS="-I/home/user/fusionseq/include"
 $ export LDFLAGS="-L/home/user/fusionseq/lib"
 </pre>

Asboner: /* Installing and configuring ROOT */

2011-05-17T18:43:58Z

Installing and configuring ROOT

← Older revision		Revision as of 18:43, 17 May 2011
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	==Installing and configuring ROOT==		==Installing and configuring ROOT==
	To install [http://root.cern.ch/drupal/ ROOT], please follow the instructions on the website. You may also include GSL library when compiling, but it is not a requirement. Once ROOT is installed, a few variables need to be defined in order to properly use this library with FusionSeq.		To install [http://root.cern.ch/drupal/ ROOT], please follow the instructions on the website. You may also include GSL library when compiling, but it is not a requirement. '''NOTE''': for Ubuntu users, the detailed instructions to install ROOT can be found [http://cometpeak.com/2011/05/building-and-installing-root-on-ubuntu-11-04-x86_64/ here].

			=====version up to 0.6.1=====
			Once ROOT is installed, a few variables need to be defined in order to properly use this library with FusionSeq.
	<pre>		<pre>
	$ export ROOTSYS=/path/to/ROOT/		$ export ROOTSYS=/path/to/ROOT/