Compiling and Installing TopHat2

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the TOPHAT2 directory:

   cd /path/to/TOPHAT2

3. Run the following command to decompress the TopHat2 installation package:

   tar xvf tophat-2.1.1.tar.gz

4. Prepare a Patch file and copy the following content to the tophat.patch file in the same directory as the tophat-2.1.1 directory.
   1. Create a tophat.patch file.

      vi tophat.patch

   2. Press i to enter the insert mode and add the following content:

      diff -uBw -aur tophat-2.1.1/src/juncs_db.cpp tophat-2.1.1-patched/src/juncs_db.cpp
      --- tophat-2.1.1/src/juncs_db.cpp   2016-02-14 19:21:17.354079000 +0100
      +++ tophat-2.1.1-patched/src/juncs_db.cpp   2016-06-02 11:26:34.097425159 +0200
      @@ -338,7 +338,7 @@
                  uint32_t left_coord = atoi(scan_left_coord);
                  uint32_t right_coord = atoi(scan_right_coord);
                  bool antisense = *orientation == '-';
      -           junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats()));
      +           junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats()));
              }
          }
       
      diff -uBw -aur tophat-2.1.1/src/tophat_reports.cpp tophat-2.1.1-patched/src/tophat_reports.cpp
      --- tophat-2.1.1/src/tophat_reports.cpp 2016-02-23 22:20:44.320710000 +0100
      +++ tophat-2.1.1-patched/src/tophat_reports.cpp 2016-06-02 11:26:22.057239478 +0200
      @@ -2705,7 +2705,7 @@
                      junction_stat.gtf_match = true;
                      junction_stat.accepted = true;
       
      -               gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
      +               gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
                  }
              }
              fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
5. Run the following command to install the patch file:

   patch -Np0 -i tophat.patch

6. Run the following command to switch to the directory generated after the package is decompressed:

   cd tophat-2.1.1

7. Run the following command to perform the configuration:

   ./configure --prefix=/path/to/TOPHAT2 --with-boost=/path/to/BOOST

8. Run the following commands to perform the compilation and installation:

   make -j 1
   make install