Installation(Outdated)

tar -xvzf rp_bin.[VERSION].tar.gz

cd rp_bin/

./rp_config

5. Enter which cluster you are using.

You can enter either the cluster name specified or the number corresponding to it. If your cluster is not listed, then specify "other".

Please enter your cluster name from the following options:

6. You need to add rp_bin/ and rp_bin/pdfjam/ to your default search path. The instructions given will vary depending on the cluster and shell you are using.

a. The configuration script will determine what shell you are using based on the SHELL variable in your environment configurations. To see this variable, type which $SHELL.

b. If you are not using bash or tcsh or are using a different cluster than Broad or GenomeDK, then you will need to determine how to add paths to your default search path on your own. When you have added rp_bin/ and rp_bin/pdfjam/ to your search path, rerun the rp_config script (./rp_config). The message given will be as follows:

Using the following cluster: other

Detected you are using the following shell: tcsh

You'll need to add the following paths to your default search path:

~/rp_bin

~/rp_bin/pdfjam

If you are using a bash shell, sample commands are located in this file: ~/rp_bin/my.bashrc_rp_path

If you are using a tcsh shell, sample commands are located in this file: ~/rp_bin/my.cshrc_rp_path

For example instructions, see http://www.cyberciti.biz/faq/unix-linux-adding-path/

If possible, add these paths permanently. Otherwise, you will need to do this everytime you start a new session.

After these directories have been added to the search path, rerun this script: ./rp_config

c. If you are using bash or tcsh and are at Broad or GenomeDK, you will receive a similar message to the one below. Run all of the commands given. These commands will append the rp_bin/ paths to your login profile and to your current session.

Using the following cluster: broad

Detected you are using the following shell: tcsh

Please run the following commands to permanently add rp_bin to the default search path:

cat ~/rp_bin/my.bashrc_rp_path >> ~/.my.bashrc

cat ~/rp_bin/my.cshrc_rp_path >> ~/.my.cshrc

set path=(~/rp_bin $path)

set path=(~/rp_bin/pdfjam $path)

./rp_config

7. Add the rp_bin/ and rp_bin/pdfjam/ directories to the search path as specified by the guidelines above and rerun rp_config:

./rp_config

8. Enter responses to the following questions:

a. You will be prompted to enter which scratch directory you want to use? Enter "y" to select the default scratch directory of /scratch/

Do you want to use the following default scratch directory? (y or n)

/scratch/

y

Using /scratch/ as the scratch directory.

Scratch directory already exists at /scratch/

b. You will be prompted to enter your two-letter initials and your email address (they will be converted to lowercase if not entered as lowercase)

Please enter your initials (2 letters):

aa

Please enter your email address:

test@email.com

c. Next, you will be asked where you want all log files to be created. (This directory is referred to as loloc throughout the site).

Do you want to use the following default directory to store your log files? (y or n)

<~/>

d. There are a number of software packages used in Ricopili. Some default paths are given for some computer clusters (i.e., LISA, Broad, GenomeDK, etc). Otherwise, you must enter the path for each software package listed here.

9. A number of files are created based on your responses.

A configuration file is created at $HOME/ricopili.conf ($HOME = your home directory)

- This contains the file paths to a number of software packages and user parameters

A number of log files are created in the log directory specified (loloc) that record all commands run:

- preimp_dir_info

- impute_dir_info

- pcaer_info

- idtager_info

- repqc2_info

- areator_info

- merge_caller_info

- postimp_navi_info

These files should never be deleted!

Creating pipeline status file to <loloc_path>//preimp_dir_info

Creating pipeline status file to <loloc_path>//impute_dir_info

Creating pipeline status file to <loloc_path>//pcaer_info

Creating pipeline status file to <loloc_path>//idtager_info

Creating pipeline status file to <loloc_path>//repqc2_info

Creating pipeline status file to <loloc_path>//areator_info

Creating pipeline status file to <loloc_path>//merge_caller_info

Creating pipeline status file to <loloc_path>//postimp_navi_info

10. If the file paths for any resource listed in $HOME/ricopili.conf does not exist, you will receive a message similar to the following:

You will need to install the binaries as described here (https://sites.google.com/a/broadinstitute.org/ricopili/resources) and use a text editor (emacs,vim,etc.) to edit the file paths listed in $HOME/ricopili.conf for the following

variables:

liloc

For instructions on how to download and install the appropriate binaries, see here.

11. Ricopili has been successfully installed if you see the following message:

Setup has been completed successfully!

If you do not receive an email with the subject rp_config, please check your email address is entered correctly at <~/> ricopili.conf

-------------------------------------------------------------------

if you see this you are good to go for the pipeline!

12. You should also receive an email with a success message verifying the email address you provided is correct.

If you do not receive an email, use a text editor to edit the email address listed in the line starting with "email" in your $HOME/ricopili.conf file.

13. If you rerun the rp_config script:

You will be prompted whether you wish to overwrite $HOME/ricopili.conf.

- Answer with either y or n.

- If you answer yes (y), a copy of the original file will be created at $HOME/ricopili.conf.copy

Updating the Ricopili Binary

Follow the instructions below if you wish to download and install a new version of Ricopili.

wget https://sites.google.com/a/broadinstitute.org/ricopili/download/rp_bin.[VERSION].tar.gz

2. Decompress a .tar.gz file using the following command:

tar -xvzf rp_bin.[VERSION].tar.gz

3. Change the current directory to the newly created rp_bin/ directory (check what the correct path is based on the tar/zip extraction).

cd rp_bin/

./rp_config

5. Assuming Ricopili has been successfully installed before, you will be prompted if you want to uninstall Ricopili.

If you answer yes or <y>, depending on the shell you are using, you will see something similar to the following message:

To uninstall Ricopili, we detect you need to remove the following paths from your default search path:

~/rp_bin/pdfjam

~/rp_bin

If this seems incorrect, DO NOT continue with the uninstall instructions below!!!

----------------------------------------------------

1. Please enter the following command to remove rp_bin from the search path for this session:

setenv PATH /broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.15.3/lib64/R/library/snow:/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.15.2/bin

----------------------------------------------------

2. To remove rp_bin permanently from the default search path in bash, run the following command:

mv my.bashrc_minus_rpbin.txt ~/.my.bashrc

which will delete the following lines from your /home/unix/jigold/.my.bashrc file:

PATH=~/rp_bin:$PATH

PATH=~/rp_bin/pdfjam:$PATH

A copy of ~/.my.bashrc is available at my.bashrc.copy

----------------------------------------------------

3. To remove rp_bin permanently from the default csh or tcsh search path, run the following command:

mv my.cshrc_minus_rpbin.txt ~/.my.cshrc

which will delete the following lines from your ~/.my.cshrc file:

set path=(~/rp_bin $path)

set path=(~/pdfjam $path)

A copy of ~/.my.cshrc is available at my.cshrc.copy

Non-Broad or Non-GenomeDK users will see a message similar to the following:

Detected you are using the following shell: bash

Warning! Ricopili is already installed.

Do you wish to uninstall Ricopili? <y/n>

y

To uninstall Ricopili, we detect you need to remove the following paths from your default search path:

~/rp_bin/pdfjam

~/rp_bin

If this seems incorrect, DO NOT continue with the uninstall instructions below!!!

----------------------------------------------------

1. Please enter the following command to remove rp_bin from the search path for this session:

export PATH=/broad/software/free/Linux/redhat_5_x86_64/pkgs/rpy2_2.2.2-python-2.6.5/bin:/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.11.0/bin:/broad/software/free/Linux/redhat_5_x86_64/pkgs/openmpi_1.4/bin

----------------------------------------------------

2. Remove the directories listed above from the some place where you permanently added the directories to the search path.

----------------------------------------------------

3. Restart this script with the following command:

./rp_config

If you answer no <n>, the script will continue with Step 6 above.

6. Follow the directions given, entering the specified commands on your own.

You want to remove all rp_bin directories from both the current search path as well as the permanent default search path. For Broad users, this entails modifying your hidden settings files: ~/.my.bashrc and ~/.my.cshrc

7. To determine whether you successfully removed all rp_bin directories from the search path, rerun the rp_config script.

./rp_config

If successful, you will be given the set of instructions to add rp_bin to the search path, starting from Step 4 above.

8. If desired, remove the old (uninstalled!) rp_bin directory.

rm -r rp_bin_old/

For Broad users, note that copies of your old hidden settings files (~/.my.bashrc and ~/.my.cshrc) are located in this directory at my.bashrc.copy and my.cshrc.copy. You may want to move these somewhere safe before deleting the entire directory.

Alternative Installation

1. Download the latest .zip from GitHub (https://github.com/Nealelab/ricopili) to somewhere you have read/write access to or just use wget (just be sure that the directory is empty).

Also you don't have to de-install older versions before re-installing a newer version. Installing from GitHub has the advantage of making it easier to test code in development, propose changes, and download minor updates. To install from

github, run the following code in place of steps 2-4 in the instructions above:

wget https://github.com/Nealelab/ricopili/archive/master.zip

Unzip the .zip file using the following command:

unzip master

The rest of the process remains unchanged.

Additional Software Packages

If you are using the Broad cluster, then the following binary paths are already installed, and you do not need to do anything else. There are likewise pre-specified binary paths on the LISA, Computerome, co-ipsych, genomedk, mssm, and uppmax clusters.