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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Unable to load stringtie in Linux #326

Closed kchen96 closed 3 years ago

kchen96 commented 3 years ago

Hi, I installed stringtie on a linux system via:

git clone https://github.com/gpertea/stringtie cd stringtie make release

And I got a few warnings, not sure if the installation was successful

cd ./samtools-0.1.18 && make lib make[1]: Entering directory/wynton/home/jainlab/kchen96/stringtie/samtools-0.1.18' gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam.c -o bam.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam.c -o sam.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. razf.c -o razf.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:11:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] bam_header_t *old; ^ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[1]: Leaving directory /wynton/home/jainlab/kchen96/stringtie/samtools-0.1.18' g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GBase.cpp -o gclib/GBase.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GStr.cpp -o gclib/GStr.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GBam.cpp -o gclib/GBam.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/gdna.cpp -o gclib/gdna.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/codons.cpp -o gclib/codons.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/gff.cpp -o gclib/gff.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c rlink.cpp -o rlink.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c tablemaker.cpp -o tablemaker.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c tmerge.cpp -o tmerge.o g++ -g -O3 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -pthread -c stringtie.cpp -o stringtie.o g++ -g -L./samtools-0.1.18 -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GBam.o gclib/gdna.o gclib/codons.o gclib/GFastaIndex.o gclib/GFaSeqGet.o gclib/gff.o gclib/GThreads.o rlink.o tablemaker.o tmerge.o stringtie.o -pthread -lbam -lz

After installation, I tried to run the program on the test data. However, I got 'stringtie: command not found'.

gpertea commented 3 years ago

./stringtie should work, if you are trying to run it right after the make command, or you can specify the full path to the directory where the binary was "installed" (i.e. copied -- Linux basics). Beware that make release does not "install" the program, it just builds it. Proper installation usually means copying the stringtie binary in a directory which is in your shell's $PATH