minor updates

rioualen · Jun 2, 2016 · 083b74c · 083b74c
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diff --git a/doc/gene-regulation_tutorials/gene-regulation_with_IFB_cloud.Rmd b/doc/gene-regulation_tutorials/gene-regulation_with_IFB_cloud.Rmd
@@ -104,12 +104,12 @@ Here we create a folder to store the source data files and download them .
 
 ```
 ## Download input reads
-mkdir -p ~/mydisk/GSE20870_analysis/data/GSM521934 
-wget -v --no-clobber ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021358/SRR051929/SRR051929.sra -P ~/mydisk/GSE20870_analysis/data/GSM521934/
+mkdir -p ~/mydisk/GSE20870-analysis/data/GSM521934 
+wget -v --no-clobber ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021358/SRR051929/SRR051929.sra -P ~/mydisk/GSE20870-analysis/data/GSM521934/
 
 ## Download ChIP-seq reads
-mkdir -p ~/mydisk/GSE20870_analysis/data/GSM521935
-wget -v --no-clobber ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021359/SRR051930/SRR051930.sra -P ~/mydisk/GSE20870_analysis/data/GSM521935/
+mkdir -p ~/mydisk/GSE20870-analysis/data/GSM521935
+wget -v --no-clobber ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021359/SRR051930/SRR051930.sra -P ~/mydisk/GSE20870-analysis/data/GSM521935/
 ```
 
 
@@ -118,7 +118,7 @@ Note: the commands above can be adapted to download the data in any other direct
 ## 1.6 Run the workflow
 
 ```
-cd  ~/mydisk/GSE20870_analysis/
+cd  ~/mydisk/GSE20870-analysis/
 ln -s ~/gene-regulation-2.0 gene-regulation
 snakemake -p -s gene-regulation/scripts/snakefiles/workflows/factor_workflow.py --configfile gene-regulation/examples/GSE20870/GSE20870.yml
 ```

diff --git a/doc/gene-regulation_tutorials/gene-regulation_with_docker.Rmd b/doc/gene-regulation_tutorials/gene-regulation_with_docker.Rmd
@@ -76,21 +76,23 @@ sudo apt-get --yes install docker
 In order to execute the study case GSE20870, you should enter the following commands:  
 
 ```
-mkdir ~/GSE20870-analysis
-mkdir ~/GSE20870-analysis/data/GSM521934 ~/GSE20870-analysis/data/GSM521935
+export ANALYSIS_DIR=~/GSE20870-analysis
+mkdir $ANALYSIS_DIR
+cd $ANALYSIS_DIR
 ```
 ```
-cd ~/GSE20870-analysis/data/GSM521934
-wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021358/SRR051929/SRR051929.sra
-cd ~/GSE20870-analysis/data/GSM521935
-wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021359/SRR051930/SRR051930.sra
+mkdir data/GSM521934 
+wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021358/SRR051929/SRR051929.sra -P data/GSM521934
+
+mkdir data/GSM521934
+wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021359/SRR051930/SRR051930.sra -P data/GSM521934
 ```
 
 ## Fetch the Docker image and run it with shared folders
 
 ```
-docker pull rioualen/gene-regulation:1.0
-docker run -v ~/GSE20870-analysis/:~/GSE20870-analysis -it rioualen/gene-regulation:2.0 /bin/bash
+docker pull rioualen/gene-regulation:2.0
+docker run -v $ANALYSIS_DIR:~/GSE20870-analysis -it rioualen/gene-regulation:2.0 /bin/bash
 ```
 
 You can share as many folders as desired, using this syntax: `-v /path/on/host/:/path/on/docker/`.

diff --git a/doc/gene-regulation_tutorials/gene-regulation_with_virtualbox.Rmd b/doc/gene-regulation_tutorials/gene-regulation_with_virtualbox.Rmd
@@ -246,9 +246,17 @@ Reboot again to see the new display.
 
 Once in the virtual machine, you can install the required programs from a terminal. 
 
+## Create a base directory for the analysis
+
+```
+export ANALYSIS_DIR="~/GSE20870-analysis"
+mkdir $ANALYSIS_DIR
+```
+
 ## Get the `gene-regulation` repository
 
 ```
+cd $ANALYSIS_DIR
 wget https://github.com/rioualen/gene-regulation/archive/2.0.tar.gz
 tar zvxf 2.0.tar.gz
 ```
@@ -258,37 +266,32 @@ tar zvxf 2.0.tar.gz
 This may take a while (30mn to 1h) & source the `.bashrc` (it's been updated with the `$PATH` for newly installed applications).
 
 ```
+cd $ANALYSIS_DIR
 make -f gene-regulation-2.0/scripts/makefiles/install_tools_and_libs.mk all
 source ~/.bashrc
 ```
 
 
 # Executing snakemake workflow example
 
-## Create study directory
-
-```
-mkdir ~/GSE20870-analysis
-cd ~/GSE20870-analysis
-```
-
 ## Download source data
 
 You can enter the following commands:
+
 ```
-mkdir -p data/GSM521934 data/GSM521935
-```
-```
-cd data/GSM521934
-wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021358/SRR051929/SRR051929.sra
-cd data/GSM521935
-wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021359/SRR051930/SRR051930.sra
+cd $ANALYSIS_DIR
+
+mkdir -p data/GSM521934
+wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021358/SRR051929/SRR051929.sra -P data/GSM521934
+
+mkdir -p data/GSM521935
+wget -nc ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX021%2FSRX021359/SRR051930/SRR051930.sra -P data/GSM521935
 ```
 
 ## Execute workflow
 
 ```
-ln -s  path/to/gene-regulation-2.0 gene-regulation
+ln -s  gene-regulation-2.0 gene-regulation
 snakemake -p -s gene-regulation/scripts/snakefiles/workflows/factor_workflow.py --configfile gene-regulation/examples/GSE20870/GSE20870.yml
 ```