PAP: Pedigree Analysis Package (Rev. 4) The Pedigree Analysis Package (PAP) is a set of FORTRAN 77 programs for computing likelihoods and simulating phenotypes of genetic models on pedigrees. Information on the Utah Info Mail facility: =========================================== To use the Utah Info Mail facilty, send mail to info@corona.med.utah.edu with one of the following "Subject" line(s): PAP Info : To receive a help/info file. PAP Query : To ask a question about PAP. PAP Error : To send an error report. Information on obtaining PAP (Rev. 4): ====================================== You may use either gopher or ftp to obtain a copy of the PAP (v4.0) source code, the users' manual in postscript format, and examples. The ftp instructions follow: Section 1: Introduction ________________________________________________________________ This document describes how to obtain a copy of the PAP source code and users manual using FTP (File Transfer Protocol) and the INTERNET. This guide assumes access to the INTERNET and familarity with INTERNET concepts and with FTP. The commands are given in UNIX and may require modification for other operating systems. Section 2 summarizes the transfer steps for the experienced user. Section 3 provides detailed step by step instructions for the less experienced user. The following tables summarize the PAP FTP information. FTP Login Information ---------------------------------------------------------------- Internet Name : ftp.genetics.utah.edu Internet Number : 155.100.232.15 Login Username : anonymous Login Password : Directory : pub/software/pap ---------------------------------------------------------------- FTP File Transfer Information ---------------------------------------------------------------- Name Size Type Transfer Mode ---------------------------------------------------------------- README.FTP 9277 ASCII Text ascii pap.tar.Z ~450000 Compressed tar file image (binary) ---------------------------------------------------------------- Section 2: Summarized Transfer Instructions ________________________________________________________________ The following table lists the steps to transfer the PAP files and prepare them for installation. The actual commands depend upon your FTP software, but the commands used below are the most commonly available. The PAP files are written to the tar file with the directory prefix of "./pap", therefore, when installing PAP, you should move to the "parent" directory of the directory in which you want PAP installed. For example, if you want to install PAP in "/usr/local/pap/..." then you should "cd" to "/usr/local" to install it. Condensed Transfer Steps ---------------------------------------------------------------- Command Description ---------------------------------------------------------------- cd Move to the PAP parent directory ftp corona.med.utah.edu Establish connection to PAP FTP server {Username:} anonymous Login as "anonymous" {Password:} Use your last name as a password cd pub/software/pap Move to the PAP directory image Set transfer mode to image (binary) get pap.tar.Z Transfer PAP compressed tar file quit Exit FTP program uncompress pap.tar.Z Restore tar file tar xvf pap.tar . Extract PAP files from tar file ---------------------------------------------------------------- Section 3: Detailed Transfer Instructions ________________________________________________________________ Step 1 - Logging in to the ROOT account If PAP will be used by more than one user, then a "system wide" installation should be made. To accomplish this, first log into your system as "root". This will enable you to install PAP in system or root directories. This will also enable you to set the appropriate file protections. Step 2 - Moving to the PAP parent directory Move to the parent directory of the directory in which you want PAP installed. For example, if you want to install PAP in "/usr/local/pap...", then "cd" to "/usr/local. The PAP tar file was built with the path "./pap/" prefixed to all files. For example at the prompt (in this case "%") type: % cd /usr/local Step 3 - Transferring PAP files using FTP This step involves using FTP to perform the file transfers. The actual FTP commands that you will use may vary from the ones used below. Consult your network manager or your FTP documentation if these commands do not work. 3a. Establishing a connection to the PAP FTP Server In order to transfer the PAP files, you must first establish a connection to the PAP FTP server. To establish a connection, type the following command at the prompt: % ftp corona.med.utah.edu 3b. Logging in to the PAP FTP Server Once the connection has been established, you must log in to the PAP FTP server. When asked for a user name, enter "anonymous". Use your last name as the password. For example: Name (corona.med.utah.edu:pc): anonymous Password (corona.med.utah.edu:anonymous): 3c. Changing the working directory You must now move to the PAP distribution directory. To change to this directory, type the following command at the FTP prompt (in this case "ftp>"): ftp> cd pub/software/pap 3d. Changing the transfer type The PAP tar file MUST be transferred as a "binary" or "image" file. Most (if not all) FTP programs default to "ASCII" file transfers. It is therefore necessary to change the FTP transfer type to "image". To change to image transfer mode, type the following command at the FTP prompt: ftp> image 3e. Transferring the PAP tar file To transfer the PAP compressed "tar" file, type the following command at the FTP prompt: ftp> get pap.tar.Z 3f. Exiting the FTP session To exit the FTP session, type the following command at the FTP prompt: ftp> quit Step 4 - Restoring PAP tar file To reduce transfer time, the PAP tar file was "compressed" after the tar file was built. It is therefore, necessary to "uncompress" the tar file once it has been transferred. To "uncompress" this file, type the following command at the prompt: % uncompress pap.tar.Z The uncompress utility converts "pap.tar.Z" to "pap.tar" ("pap.tar.Z" is removed during this conversion). If you wish to save the compressed form of the PAP tar file, you must do so BEFORE invoking the uncompress utility. Step 5 - Extracting PAP files To extract the PAP files from the tar file, type the following command at the prompt: % tar xvf pap.tar . The tar utility will extract each PAP file and place it in "./pap" directory. Step 6 - Saving and/or removing the PAP tar file Once the PAP files have been extracted, it is not necessary to keep the tar file. However, this tar file can serve as an initial backup of PAP. You may want to save the tar file for this purpose. Placing this file on a tape or other backup media is strongly suggested. Consult your system manager or your system documentation for the appropriate way for performing this backup. Once this has been performed, you may delete the tar file by typing the following command at the prompt: % rm pap.tar