Installing PHRED in the right way

2008-07-08
2013-04-18
  • I am using the package normally and it is working perfectly using EBA. Now I obtain Phred and I installed it on my PC. But PreGap4 seems to not work with Phred. Maybe I install Phred in a wrong folder… Please could you explain me where I have to install Phred because from Staden Manual I can't obtain this information.
    Thank you for answering to me,
    Filip

     
    • Perfect! Surfing on Internet I found this site that explains everything: http://www.phineus.org/installation/phred.html. It is what I was looking for! It may be useful for everyone.
      Filip

       
    • Hi,

      I am having a error when I try to run pregap4. I am doing a very simple example with a few reads.
      - Report from 'Enter assemble (into Gap4)' -
      ERR: Failed to open database teste.0
      ERR: "invalid command name "open_db""
      ERR: Aborting.

      I am trying to figure out what is wrong. Thus, I checked the file: gap.tcl in /lib/.

      The file indicate that is using IO.
          #open database
          set origtype $licence(type)
          set io [open_db -name $db_name -version $version_num -access $access \             -create $create]

          if {"$io" == ""} {
      #       puts "ERROR: Couldn't open the database '$db_name.$version_num' - exiting."
      #       6/1/99 johnt - use verror so message is shown with Windows NT
              if {$licence(type) == "d"} {
                  verror ERR_FATAL "Gap4" "ERROR: Demonstration mode could not open this database. Try \"gap4viewer\" instead."
              } else {       
                  verror ERR_FATAL "Gap4" "ERROR: Couldn't open the database '$db_name.$version_num' - exiting."
              }
             
              exit

      Checking IO files I found:
      Basic Gap4 I/O

      This level contains the basic functions for reading, writing, creation and deletion of the Gap4 structures, such as readings and templates as well as higher level functions built on top of these. It is this level of code that should generally be used by the programmer. The implementation of this level has function code and prototypes spread over a variety of files, but the programmer should only #include the `IO.h' file.

      The primary functions are:

      `IO.c'

          open_db
          close_db
          del_db
              Opening/creation, closing and deletion of databases.
          GT_Read, GT_Write, GT_Write_cached
          TextRead, TextAllocRead, TextWrite
          DataRead, DataWrite
          ArrayRead, ArrayWrite
          BitmapRead, BitmapWrite

      I try to locate the IO.c in my cpu and I could only find it in the STADEN src code. However, I am using a compiled version. Where are the IO functions in staden-linux-x86_64-1-7-1b.tar.gz ?

      Can someone give me a hint ?