Issue at installation (Trinity v.2.15.2)

[FungAx]

I have tried many versions of trinity and i have updated everything i could on my machine (including OS).

During the installation this problem appears :

cd htslib git submodule init && git submodule update fatal: not a git repository (or any of the parent directories): .git mkdir -p build autoheader autoconf ./configure --prefix=pwd/build/ configure: error: cannot find required auxiliary files: config.guess config.sub make[2]: [Makefile:10: htslib/version.h] Error 1 make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/bamsifter' make[1]: [Makefile:31: bamsifter_target] Error 2 make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins' make: *** [Makefile:39: trinity_essentials] Error 2

If anyone has any idea what is going wrong , some advice would be much appreciated I'm sorry if my report isn't well structured , I'm new to this.

Full log:

$ make Using gnu compiler for Inchworm and Chrysalis cd Inchworm && make make[1]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm' mkdir -p build cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- No build type specified so building in RELEASE mode. -- system: Linux -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' [ 35%] Built target inchworm make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' [ 67%] Built target FastaToDeBruijn make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' [100%] Built target fastaToKmerCoverageStats make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' Install the project... -- Install configuration: "Release" -- Up-to-date: ../bin/inchworm -- Up-to-date: ../bin/FastaToDeBruijn -- Up-to-date: ../bin/fastaToKmerCoverageStats make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm' cd Chrysalis && make make[1]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis' mkdir -p build cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- No build type specified so building in RELEASE mode. -- system: Linux -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 14%] Built target Chrysalis make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 34%] Built target GraphFromFasta make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 52%] Built target QuantifyGraph make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 68%] Built target ReadsToTranscripts make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 88%] Built target BubbleUpClustering make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [100%] Built target CreateIwormFastaBundle make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' Install the project... -- Install configuration: "Release" -- Up-to-date: ../bin/Chrysalis -- Up-to-date: ../bin/GraphFromFasta -- Up-to-date: ../bin/QuantifyGraph -- Up-to-date: ../bin/ReadsToTranscripts -- Up-to-date: ../bin/BubbleUpClustering -- Up-to-date: ../bin/CreateIwormFastaBundle make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis' cd trinity-plugins && make trinity_essentials make[1]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins' cd seqtk-trinity && make CXX=g++ CC=gcc make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/seqtk-trinity' gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk-trinity -lz -lm make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/seqtk-trinity' mv seqtk-trinity/seqtk-trinity ./BIN/. cd "ParaFly" && sh ./configure --prefix=pwd CXX=g++ CC=gcc CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && make install && \ cp bin/ParaFly ../BIN/ checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes 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 g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for g++ option to support OpenMP... none needed checking for library containing cos... none required configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' Making install in src make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' test -z "/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/bin" || /usr/bin/mkdir -p "/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/bin" /usr/bin/install -c ParaFly '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' ln -sf Trimmomatic-0.36 Trimmomatic cd bamsifter && make make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/bamsifter' ./build_htslib.sh

cd htslib git submodule init && git submodule update fatal: not a git repository (or any of the parent directories): .git mkdir -p build autoheader autoconf ./configure --prefix=pwd/build/ configure: error: cannot find required auxiliary files: config.guess config.sub make[2]: [Makefile:10: htslib/version.h] Error 1 make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/bamsifter' make[1]: [Makefile:31: bamsifter_target] Error 2 make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins' make: *** [Makefile:39: trinity_essentials] Error 2

[brianjohnhaas]

Hi,

The very latest version of trinity should deal with bamsifter compilation issues - at least it did with certain linux distros.

I wouldn't bother compiling anything.... just use the singularity image (or docker) if possible. https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker#running-trinity-using-singularity

On Tue, Sep 10, 2024 at 1:13 AM FungAx @.***> wrote:

I have tried many versions of trinity and i have updated everything i could on my machine (including OS).

During the installation this problem appears :

cd htslib git submodule init && git submodule update fatal: not a git repository (or any of the parent directories): .git mkdir -p build autoheader autoconf ./configure --prefix=pwd/build/ configure: error: cannot find required auxiliary files: config.guess config.sub make[2]: [Makefile:10: htslib/version.h] Error 1 make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/bamsifter' make[1]: [Makefile:31: bamsifter_target] Error 2 make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins' make: *** [Makefile:39: trinity_essentials] Error 2

If anyone has any idea what is going wrong , some advice would be much appreciated I'm sorry if my report isn't well structured , I'm new to this.

Full log:

$ make Using gnu compiler for Inchworm and Chrysalis cd Inchworm && make make[1]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm' mkdir -p build cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- No build type specified so building in RELEASE mode. -- system: Linux -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' [ 35%] Built target inchworm make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' [ 67%] Built target FastaToDeBruijn make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' [100%] Built target fastaToKmerCoverageStats make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' Install the project... -- Install configuration: "Release" -- Up-to-date: ../bin/inchworm -- Up-to-date: ../bin/FastaToDeBruijn -- Up-to-date: ../bin/fastaToKmerCoverageStats make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm/build' make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Inchworm' cd Chrysalis && make make[1]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis' mkdir -p build cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- No build type specified so building in RELEASE mode. -- system: Linux -- Configuring done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 14%] Built target Chrysalis make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 34%] Built target GraphFromFasta make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 52%] Built target QuantifyGraph make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 68%] Built target ReadsToTranscripts make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [ 88%] Built target BubbleUpClustering make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' [100%] Built target CreateIwormFastaBundle make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' Install the project... -- Install configuration: "Release" -- Up-to-date: ../bin/Chrysalis -- Up-to-date: ../bin/GraphFromFasta -- Up-to-date: ../bin/QuantifyGraph -- Up-to-date: ../bin/ReadsToTranscripts -- Up-to-date: ../bin/BubbleUpClustering -- Up-to-date: ../bin/CreateIwormFastaBundle make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis/build' make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/Chrysalis' cd trinity-plugins && make trinity_essentials make[1]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins' cd seqtk-trinity && make CXX=g++ CC=gcc make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/seqtk-trinity' gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk-trinity -lz -lm make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/seqtk-trinity' mv seqtk-trinity/seqtk-trinity ./BIN/. cd "ParaFly" && sh ./configure --prefix=pwd CXX=g++ CC=gcc CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && make install && cp bin/ParaFly ../BIN/ checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes 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 g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for g++ option to support OpenMP... none needed checking for library containing cos... none required configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' Making install in src make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' test -z "/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/bin" || /usr/bin/mkdir -p "/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/bin" /usr/bin/install -c ParaFly '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly/src' make[3]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[4]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[3]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/ParaFly' ln -sf Trimmomatic-0.36 Trimmomatic cd bamsifter && make make[2]: Entering directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/bamsifter' ./build_htslib.sh

cd htslib git submodule init && git submodule update fatal: not a git repository (or any of the parent directories): .git mkdir -p build autoheader autoconf ./configure --prefix=pwd/build/ configure: error: cannot find required auxiliary files: config.guess config.sub make[2]: [Makefile:10: htslib/version.h] Error 1 make[2]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins/bamsifter' make[1]: [Makefile:31: bamsifter_target] Error 2 make[1]: Leaving directory '/home/apa/Downloads/trinityrnaseq-v2.15.2.FULL/trinityrnaseq-v2.15.2/trinity-plugins' make: *** [Makefile:39: trinity_essentials] Error 2

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas