Recent changes to clinical_pathoscope

clinical_pathoscope modified by Allyson Byrd

Allyson Byrd — Thu, 17 Apr 2014 13:45:14 -0000

--- v12
+++ v13
@@ -9,7 +9,7 @@
 1. Installation
 ---------------

-1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.2.tar.gz/download
+1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.3.tar.gz/download

 + Extract the code to a separate folder
 You could issue the following command to extract the files:

clinical_pathoscope modified by Allyson Byrd

Allyson Byrd — Thu, 17 Apr 2014 13:41:17 -0000

--- v11
+++ v12
@@ -13,7 +13,7 @@

 + Extract the code to a separate folder
 You could issue the following command to extract the files:
-"tar xvf clinical_pathoscope_vXXX.tar.gz"
+"tar xvf clinical_pathoscope_v1.0.3.tar.gz"

 + Download bowtie2 from http://sourceforge.net/projects/bowtie-bio/

clinical_pathoscope modified by Solaiappan Manimaran

Solaiappan Manimaran — Wed, 16 Apr 2014 00:11:23 -0000

--- v10
+++ v11
@@ -19,7 +19,7 @@

 + Example sample fastq file can be downloaded from http://sourceforge.net/projects/pathoscope/files/simulated_sample.fastq.gz/download

-+ Reference databases (human, viral, & bacterial) as well as their associated alignment indexes can be downloaded from 
++ Reference databases (human, viral, & bacterial) as well as their associated alignment indexes can be downloaded from 

 2. Running

clinical_pathoscope modified by Solaiappan Manimaran

Solaiappan Manimaran — Tue, 15 Apr 2014 19:33:02 -0000

--- v9
+++ v10
@@ -19,7 +19,7 @@

 + Example sample fastq file can be downloaded from http://sourceforge.net/projects/pathoscope/files/simulated_sample.fastq.gz/download

-+ Reference databases (human, viral, & bacterial) as well as their associated alignment indexes can be downloaded from 
++ Reference databases (human, viral, & bacterial) as well as their associated alignment indexes can be downloaded from 

 2. Running

clinical_pathoscope modified by Solaiappan Manimaran

Solaiappan Manimaran — Mon, 14 Apr 2014 17:00:04 -0000

--- v8
+++ v9
@@ -9,11 +9,11 @@
 1. Installation
 ---------------

-1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.1.tar.gz/download
+1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.2.tar.gz/download

 + Extract the code to a separate folder
 You could issue the following command to extract the files:
-"tar xvf clinical_pathoscope_v1.0.1.tar.gz"
+"tar xvf clinical_pathoscope_vXXX.tar.gz"

 + Download bowtie2 from http://sourceforge.net/projects/bowtie-bio/

clinical_pathoscope modified by Joseph Perez-Rogers

Joseph Perez-Rogers — Mon, 18 Nov 2013 21:12:49 -0000

--- v7
+++ v8
@@ -9,11 +9,11 @@
 1. Installation
 ---------------

-1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.tar.gz/download
+1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.1.tar.gz/download

 + Extract the code to a separate folder
 You could issue the following command to extract the files:
-"tar xvf clinical_pathoscope_v1.0.tar.gz"
+"tar xvf clinical_pathoscope_v1.0.1.tar.gz"

 + Download bowtie2 from http://sourceforge.net/projects/bowtie-bio/

clinical_pathoscope modified by Joseph Perez-Rogers

Joseph Perez-Rogers — Mon, 18 Nov 2013 21:07:43 -0000

--- v6
+++ v7
@@ -29,9 +29,9 @@

 + Change directory to where you extracted the code 

-+ Create a config file by filling in the necessary information shown in example_config.txt
++ Create a config file by filling in the necessary information shown in config.txt

-+ Simply run run_clinical_pathoscope.py with the config file to generate the shell script to run Clinical Pathoscope for a particular sample ("python run_clinical_pathoscope.py config.txt")
++ Simply run runClinicalPathoscope.py with the config file to generate the shell script to run Clinical Pathoscope for a particular sample ("python runClinicalPathoscope.py config.txt")

 3. Output Files
 ---------------

clinical_pathoscope modified by Solaiappan Manimaran

Solaiappan Manimaran — Mon, 11 Nov 2013 17:31:40 -0000

--- v5
+++ v6
@@ -19,7 +19,7 @@

 + Example sample fastq file can be downloaded from http://sourceforge.net/projects/pathoscope/files/simulated_sample.fastq.gz/download

-+ Reference databases (human, viral, & bacterial) as well as their associated alignment indexes can be downloaded from ftp://oligomer.bumc.bu.edu/data/databases.tar.gz
++ Reference databases (human, viral, & bacterial) as well as their associated alignment indexes can be downloaded from 

 2. Running

clinical_pathoscope modified by Solaiappan Manimaran

Solaiappan Manimaran — Mon, 11 Nov 2013 15:51:47 -0000

--- v4
+++ v5
@@ -75,7 +75,7 @@

 1. Clincal Pathoscope comes bundled with the original Pathoscope (Version 1.0 ), 3 prebuilt bowtie2 databases for human, bacteria, and virus, and our 1 simulated dataset. 

-+ The human host library consisted of two sequences; the GRCh37/hg19 build of the human genome, as well as the human ribosomal DNA sequence [GenBank:U13369]. 
++ The human host library consisted of two sequences; the GRCh37/hg19 build of the human genome, as well as the human ribosomal DNA sequence (GenBank:U13369). 

 + The bacterial library was downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz, 12/15/12).

clinical_pathoscope modified by Solaiappan Manimaran

Solaiappan Manimaran — Mon, 11 Nov 2013 15:50:41 -0000

--- v3
+++ v4
@@ -9,11 +9,11 @@
 1. Installation
 ---------------

-1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope.tar.gz/download
+1. Download Clinical Pathoscope code from http://sourceforge.net/projects/pathoscope/files/clinical_pathoscope_v1.0.tar.gz/download

 + Extract the code to a separate folder
 You could issue the following command to extract the files:
-"tar xvf clinical_pathoscope.tar.gz"
+"tar xvf clinical_pathoscope_v1.0.tar.gz"

 + Download bowtie2 from http://sourceforge.net/projects/bowtie-bio/