jerryyyyy
commented
6 years ago Hi, I got this to work about 2 months ago and am back in the same boat with a new install. I have admin privileges but my bamtools install does not seem to put the libraries in the right spot (I cannot find them) in the format/location required, in other words, I do not find the proper directories to be referenced in the ./configure script.
The /usr/local/include/bamtools has /shared and /api directories now...
your instructions
The executable binary will be at src/Telseq/telseq. If bamtools are installed not at the system location, you can specify their location by
./configure --with-bamtools=/path/to/bamtools
The /path/to/bamtools directory is the directory that contains 'lib' and 'include' sub directories.
zd1
What specific files are needed to copy over to make telseq work? I'm on a cluster (one of the largest in the world) and can't get admin access. I tried using the bamtools paths, but to no avail. bash-4.1$ ./configure --with-bamtools=/usr/local/apps/bamtools/2.4.1/lib --prefix=bash-4.1$ ./configure --with-bamtools=/usr/local/apps/bamtools/2.4.1/lib configure: WARNING: you should use --build, --host, --target configure: WARNING: invalid host type: ./configure configure: error: expected an absolute directory name for --prefix: bash-4.1$ bash-4.1$ ./configure --with-bamtools=/usr/local/apps/bamtools/2.4.1/lib/ --prefix=/usr/local/apps/bamtools/2.4.1/lib/ checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... no checking for sys/stat.h... no checking for stdlib.h... no checking for string.h... no checking for memory.h... no checking for strings.h... no checking for inttypes.h... no checking for stdint.h... no checking for unistd.h... no checking api/BamReader.h usability... no checking api/BamReader.h presence... yes configure: WARNING: api/BamReader.h: present but cannot be compiled configure: WARNING: api/BamReader.h: check for missing prerequisite headers? configure: WARNING: api/BamReader.h: see the Autoconf documentation configure: WARNING: api/BamReader.h: section "Present But Cannot Be Compiled" configure: WARNING: api/BamReader.h: proceeding with the compiler's result configure: WARNING: ## ------------------------------------ ## configure: WARNING: ## Report this to zhihao.ding@gmail.com ## configure: WARNING: ## ------------------------------------ ## checking for api/BamReader.h... no configure: error: The bamtools library must be installed (http://github.com/pezmaster31/bamtools). You can specify its path with the --with-bamtools=PATH option