Recent changes to INSTALL

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 12:37:39 -0000

--- v12
+++ v13
@@ -12,7 +12,6 @@
 * *Fold* and *bifold* tools (text interfaces) from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html 
     * Don't forget to set the DATAPATH environment variable: http://rna.urmc.rochester.edu/Text/Thermodynamics.html
 * R: https://www.r-project.org/ 
-* 
 * Statistics::R Perl module
 * You will also need to have Perl intalled

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 12:37:13 -0000

--- v11
+++ v12
@@ -12,6 +12,7 @@
 * *Fold* and *bifold* tools (text interfaces) from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html 
     * Don't forget to set the DATAPATH environment variable: http://rna.urmc.rochester.edu/Text/Thermodynamics.html
 * R: https://www.r-project.org/ 
+* 
 * Statistics::R Perl module
 * You will also need to have Perl intalled

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 12:36:19 -0000

--- v10
+++ v11
@@ -1,8 +1,6 @@
 http://homer.salk.edu/homer/introduction/install.html#Installing_3rd_Party_Software

 The commands gs, seqlogo, blat, and samtools should now work from the command line (if they don't and you think they should, remember to type: source ~/.bash_profile)
-
-

 # Introduction
 ASSA is a pipeline for large scale RNA-RNA interaction prediction that utilizes thermodymanics tools from the RNAstructure package.
@@ -11,7 +9,8 @@
 To use ASSA, you will need to install:

 * *blastn*: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
-* *Fold* and *bifold* tools (text interfaces) from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
+* *Fold* and *bifold* tools (text interfaces) from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html 
+    * Don't forget to set the DATAPATH environment variable: http://rna.urmc.rochester.edu/Text/Thermodynamics.html
 * R: https://www.r-project.org/ 
 * Statistics::R Perl module
 * You will also need to have Perl intalled

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 12:31:42 -0000

--- v9
+++ v10
@@ -37,7 +37,7 @@
    Fold _7SL.fna _7SL.ct

 5) To run ASSA on the sample sequences using 4 CPUs you can type:
-   assa.pl --num_threads 4 _7SL.fna _TP53.fna > _out.assa
+   assa.pl _7SL.fna _TP53.fna > _out.assa

 # Enabling more ASSA options

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 12:06:15 -0000

--- v8
+++ v9
@@ -18,11 +18,11 @@

 # ASSA Installation Instructions
 1) Make sure that you have ~/bin (where ~ is your home directory) in your $PATH environment variable by typing "echo $PATH".
-   If it is not there add the following line in your ~/.bash_profile and re-login:
+   If it is not there add the following line in your ~/.bash_profile and type "source ~/.bash_profile":
    export PATH=$PATH:$HOME/bin

 2) Add the ~/bin folder (or any other location) to the list of directories for Perl modules.
-   Add the following line in your ~/.bash_profile and re-login:
+   Add the following line in your ~/.bash_profile and type "source ~/.bash_profile":
    export PERL5LIB=$PERL5LIB:$HOME/bin

 3) Install ASSA:

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 11:54:02 -0000

--- v7
+++ v8
@@ -11,7 +11,7 @@
 To use ASSA, you will need to install:

 * *blastn*: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
-* *Fold* and *bifold* tools from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
+* *Fold* and *bifold* tools (text interfaces) from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
 * R: https://www.r-project.org/ 
 * Statistics::R Perl module
 * You will also need to have Perl intalled

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 11:51:25 -0000

--- v6
+++ v7
@@ -7,22 +7,14 @@
 # Introduction
 ASSA is a pipeline for large scale RNA-RNA interaction prediction that utilizes thermodymanics tools from the RNAstructure package.

-Prerequisites
-===
+# Prerequisites
 To use ASSA, you will need to install:

-* blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
-* b
-* c
-
-* 
-* Fold and bifold tools from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
-* 
-* 
-* R: https://www.r-project.org/
+* *blastn*: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
+* *Fold* and *bifold* tools from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
+* R: https://www.r-project.org/ 
 * Statistics::R Perl module
 * You will also need to have Perl intalled
-

 # ASSA Installation Instructions
 1) Make sure that you have ~/bin (where ~ is your home directory) in your $PATH environment variable by typing "echo $PATH".

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 11:50:19 -0000

--- v5
+++ v6
@@ -10,6 +10,7 @@
 Prerequisites
 ===
 To use ASSA, you will need to install:
+
 * blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 * b
 * c

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 11:50:00 -0000

--- v4
+++ v5
@@ -10,12 +10,11 @@
 Prerequisites
 ===
 To use ASSA, you will need to install:
-
-* a
+* blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 * b
 * c

-* blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
+* 
 * Fold and bifold tools from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
 * 
 *

INSTALL modified by Ivan Antonov

Ivan Antonov — Mon, 01 Aug 2016 11:49:42 -0000

--- v3
+++ v4
@@ -7,8 +7,14 @@
 # Introduction
 ASSA is a pipeline for large scale RNA-RNA interaction prediction that utilizes thermodymanics tools from the RNAstructure package.

-# Prerequisites
+Prerequisites
+===
 To use ASSA, you will need to install:
+
+* a
+* b
+* c
+
 * blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 * Fold and bifold tools from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
 *