added param desc and example for chr_names

03_singleFileImputation.sh

@@ -1,8 +1,8 @@
 SECONDS=0
 #Send File
-scp -i $3 ./target.vcf.gz $1:/volumes/volume001
+scp -i $2 ./target.vcf.gz $1:/volumes/volume001
 #Start imputation
-ssh -i $3 ubuntu@$1 "cd /volumes/volume001; ./singleFileImpute.sh > singleFileImpute.log 2> singleFileImpute.err;";
+ssh -i $2 ubuntu@$1 "cd /volumes/volume001; ./singleFileImpute.sh > singleFileImpute.log 2> singleFileImpute.err;";
 
 duration=$SECONDS
 echo "$(($duration/60)) minutes and $(($duration%60)) seconds elapsed"

03_start_job.sh

@@ -1 +1 @@
-ssh -i $3 ubuntu@$1 "cd /volumes/volume001; mkdir imputedOnReferencePanel; ./imputeOnReferencePanel.sh >result.log 2>result.err;"
+ssh -i $2 ubuntu@$1 "cd /volumes/volume001; mkdir imputedOnReferencePanel; ./imputeOnReferencePanel.sh >result.log 2>result.err;"

03_start_job_gt.sh

@@ -1 +1 @@
-ssh -i $3 ubuntu@$1 "cd /volumes/volume001; mkdir imputed; ./batch_impute.sh >result.log 2>result.err;"
+ssh -i $2 ubuntu@$1 "cd /volumes/volume001; mkdir imputed; ./batch_impute.sh >result.log 2>result.err;"

04_receive_data.sh

@@ -1,3 +1,3 @@
-ssh -i $3 ubuntu@$1 "cd /volumes/volume001; tar -cf imputed.tar imputed/"
-scp -i $3 $1:/volumes/volume001/imputed.tar .
+ssh -i $2 ubuntu@$1 "cd /volumes/volume001; tar -cf imputed.tar imputed/"
+scp -i $2 $1:/volumes/volume001/imputed.tar .
 tar -xf imputed.tar

05_get_log.sh

@@ -1,4 +1,4 @@
-scp -i $3 $1:/volumes/volume001/result.log .
+scp -i $2 $1:/volumes/volume001/result.log .
 mv result.log result_$1.log
-scp -i $3 $1:/volumes/volume001/result.err .
+scp -i $2 $1:/volumes/volume001/result.err .
 mv result.err result_$1.err

06_cleanup.sh

@@ -1,2 +1,2 @@
-ssh -i $3 ubuntu@$1 "cd /volumes/volume001; sudo rm -rf imputed/; sudo rm imputed.tar; sudo rm -rf imputation_set.split/; sudo rm result.*"
+ssh -i $2 ubuntu@$1 "cd /volumes/volume001; sudo rm -rf imputed/; sudo rm imputed.tar; sudo rm -rf imputation_set.split/; sudo rm result.*"
 rm imputed.tar

README.md

@@ -1,3 +1,8 @@
+# DivImpute 
+
+Scripts to start imputation jobs on the virtual machines of a project running on the de.NBI Cloud. 
+Three virtual machines are used in this particular setup. One Head Node to start the jobs by running the scripts and two Computational Nodes. All nodes run with Ubuntu and the later specified software was installed. The nodes store the data in a Cinder Volume mounted as /volumes/volume001. 
+
 ## Required Tools
 
 - [Beagle4.1](https://faculty.washington.edu/browning/beagle/b4_1.html) and bref
@@ -7,5 +12,55 @@
 
 1. Install required tools
 3. The enumerated scripts are run from a header node, that can access some computational nodes by running the scripts *batch_impute.sh* or *imputeOnReferencePanel.sh*
-4. the single node example can be accessed through the script *03_singelFileImputation.sh*
+4. the single node example can be accessed through the script *03_singleFileImputation.sh*
+
+## Parameters
+
+### 01_split.sh
+Parameter | Description | Example
+---       | ---         | ---
+$1        | Input VCF   | input.vcf.gz
+$2        | Output Name | output
+
+### 02_send_data.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | List of Chromosome Names      | chr_names.txt
+$2        | IP Address Computational Node | 192.168.0.80 
+$3        | Private Key                   | .ssh/my-private-key
+
+### 03_singleFileImputation.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | IP Address Computational Node | 192.168.0.80
+$2        | Private Key                   | .ssh/my-private-key
+
+### 03_start_job_gt.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | IP Address Computational Node | 192.168.0.80
+$2        | Private Key                   | .ssh/my-private-key
+
+### 03_start_job.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | IP Address Computational Node | 192.168.0.80
+$2        | Private Key                   | .ssh/my-private-key
+
+### 04_receive_data.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | IP Address Computational Node | 192.168.0.80
+$2        | Private Key                   | .ssh/my-private-key
+
+### 05_get_logs.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | IP Address Computational Node | 192.168.0.80
+$2        | Private Key                   | .ssh/my-private-key
 
+### 06_cleanup.sh
+Parameter | Description                   | Example
+---       | ---                           | ---
+$1        | IP Address Computational Node | 192.168.0.80
+$2        | Private Key                   | .ssh/my-private-key

examples/chr_names.txt

@@ -0,0 +1,22 @@
+chr1A
+chr1B
+chr1D
+chr2A
+chr2B
+chr2D
+chr3A
+chr3B
+chr3D
+chr4A
+chr4B
+chr4D
+chr5A
+chr5B
+chr5D
+chr6A
+chr6B
+chr6D
+chr7A
+chr7B
+chr7D
+chrUn