FusionSeq
From GersteinInfo
(→Introduction) |
|||
| (14 intermediate revisions not shown) | |||
| Line 1: | Line 1: | ||
<center>[http://rnaseq.gersteinlab.org/fusionseq/ FusionSeq main web page]</center> | <center>[http://rnaseq.gersteinlab.org/fusionseq/ FusionSeq main web page]</center> | ||
| - | + | This document provides the information for downloading, installing, compile and run FusionSeq. Please note that these tools were tested on a multi-node cluster of computing nodes with Linux Red Hat as operating system and PBS as scheduler system. FusionSeq programs are written in C and should likely compile to most Unix/Linux platforms. We used the gcc complier (version 3.4.6 20060404) to compile the source code. | |
| - | This | + | However, this is not a plug-and-play program, but it requires the user to compile, install and run a set of programs. Please read the [[Requirements|requirements]] '''before''' [[#Download|downloading]] FusionSeq. |
| - | However, this is not a plug-and-play program, but it requires the user to compile, install and run a set of programs. Please read the requirements before [[#Download|downloading]] FusionSeq. | + | |
| - | + | ||
| - | |||
| - | + | '''IMPORTANT''': Starting from version 0.7.0, we adopted a different approach to include the configuration file that allows the users to simply download the binary files for their platform. However, we still provide the source code, which now uses the more standard autoconf/automake tools, thus simplifying the installation of FusionSeq. Please note that at the time of writing (May 7th, 2011), version 0.7.0 is still in alpha. Any feedback will be very much appreciated. | |
| - | |||
| - | + | If you have any questions, please check the [[FusionSeq_FAQ|FAQ]] or send an email to [mailto:fusionseq-faq@gersteinlab.org fusionseq-faq@gersteinlab.org] | |
| - | |||
| - | + | ==[[FusionSeq Requirements]]== | |
| + | List of required programs and data. Please read this section '''before''' downloading FusionSeq. | ||
| + | |||
| + | ==[[FusionSeq Download|Download]]== | ||
| + | Links to FusionSeq source code and data sets. | ||
| + | |||
| + | ==[[Installation and Configuration of FusionSeq]]== | ||
| + | Instructions to install and configure FusionSeq. | ||
| + | |||
| + | ==[[How to execute FusionSeq]]== | ||
| + | An example workflow of FusionSeq. | ||
| + | |||
| + | ==[[FusionSeq_List of programs|List of programs]]== | ||
| + | Description of all the FusionSeq programs. | ||
| + | |||
| + | ==[[FusionSeq_Test Datasets|Test Datasets]]== | ||
| + | A few datasets to test FusionSeq installation. | ||
| + | |||
| + | ==[http://dynamic.gersteinlab.org/people/asboner/FusionSeq/geneFusions_cgi Demo]== | ||
| + | You can see some of the results of FusionSeq as described in the paper. Use the sample IDs reported in Table 1, e.g. 106_T, 1700_D. | ||
| + | |||
| + | ==[[FusionSeq_FAQ|Frequently Asked Questions (FAQ)]]== | ||
| + | Solutions to common problems. If your issue is not described in the [[FusionSeq_FAQ|FAQ]], please send an email to [mailto:fusionseq-faq@gersteinlab.org fusionseq-faq@gersteinlab.org] | ||
| + | |||
| + | ==[[FusionSeq Gallery|Gallery]]== | ||
| + | Some figures about FusionSeq. | ||
| + | |||
| + | ==[[FusionSeq_Papers|In the news et al.]]== | ||
| + | News or scientific papers referring to FusionSeq | ||
Latest revision as of 11:43, 7 May 2011
This document provides the information for downloading, installing, compile and run FusionSeq. Please note that these tools were tested on a multi-node cluster of computing nodes with Linux Red Hat as operating system and PBS as scheduler system. FusionSeq programs are written in C and should likely compile to most Unix/Linux platforms. We used the gcc complier (version 3.4.6 20060404) to compile the source code. However, this is not a plug-and-play program, but it requires the user to compile, install and run a set of programs. Please read the requirements before downloading FusionSeq.
IMPORTANT: Starting from version 0.7.0, we adopted a different approach to include the configuration file that allows the users to simply download the binary files for their platform. However, we still provide the source code, which now uses the more standard autoconf/automake tools, thus simplifying the installation of FusionSeq. Please note that at the time of writing (May 7th, 2011), version 0.7.0 is still in alpha. Any feedback will be very much appreciated.
If you have any questions, please check the FAQ or send an email to fusionseq-faq@gersteinlab.org
Contents |
FusionSeq Requirements
List of required programs and data. Please read this section before downloading FusionSeq.
Download
Links to FusionSeq source code and data sets.
Installation and Configuration of FusionSeq
Instructions to install and configure FusionSeq.
How to execute FusionSeq
An example workflow of FusionSeq.
List of programs
Description of all the FusionSeq programs.
Test Datasets
A few datasets to test FusionSeq installation.
Demo
You can see some of the results of FusionSeq as described in the paper. Use the sample IDs reported in Table 1, e.g. 106_T, 1700_D.
Frequently Asked Questions (FAQ)
Solutions to common problems. If your issue is not described in the FAQ, please send an email to fusionseq-faq@gersteinlab.org
Gallery
Some figures about FusionSeq.
In the news et al.
News or scientific papers referring to FusionSeq
