Problem installing STAR on Mac OSX

Question

[biomagician]

Dear Community,

I am having issues install STAR (https://github.com/alexdobin/STAR). I follow the procedure here:

https://github.com/alexdobin/STAR So for Mac:

Get STAR source using git

git clone https://github.com/alexdobin/STAR.git (works fine)

cd STAR

Build STAR

cd source

make STARforMacStatic CXX=/usr/bin/gcc (does not work)

Error message:

Makefile:91: Depend.list: No such file or directory /Applications/Xcode.app/Contents/Developer/usr/bin/make -C htslib lib-static cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c bgzf.c:68:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ ./htslib/khash.h:599:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t h... ^ <scratch space="">:21:1: note: expanded from here kh_clear_cache ^ 1 warning generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c faidx.c:21:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h... ^ <scratch space="">:325:1: note: expanded from here kh_clear_s ^ faidx.c:21:1: warning: unused function 'kh_del_s' [-Wunused-function] ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:339:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x... ^ <scratch space="">:11:1: note: expanded from here kh_del_s ^ 2 warnings generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "0.0.1"' > version.h cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c hts.c:19:5: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT2(, BGZF, bgzf_read, 65536) ^ ./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2' __KS_INLINED(__read) ^ ./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED' static inline int ks_getc(kstream_t *ks) \ ^ hts.c:448:1: warning: unused function 'kh_clear_bin' [-Wunused-function] KHASH_MAP_INIT_INT(bin, bins_t) ^ ./htslib/khash.h:584:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h... ^ <scratch space="">:34:1: note: expanded from here kh_clear_bin ^ 2 warnings generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o sam.o sam.c sam.c:1335:1: warning: unused function 'kh_clear_olap_hash' [-Wunused-function] KHASH_MAP_INIT_STR(olap_hash, lbnode_t *) ^ ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h... ^ <scratch space="">:216:1: note: expanded from here kh_clear_olap_hash ^ 1 warning generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c vcf.c:15:1: warning: unused function 'kh_clear_vdict' [-Wunused-function] KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) ^ ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h... ^ <scratch space="">:325:1: note: expanded from here kh_clear_vdict ^ vcf.c:15:1: warning: unused function 'kh_del_vdict' [-Wunused-function] ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str... ^ ./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map... ^ ./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu... ^ ./htslib/khash.h:339:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x... ^ <scratch space="">:10:1: note: expanded from here kh_del_vdict ^ 2 warnings generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c /bin/rm -f ./Depend.list /usr/bin/gcc -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 8 Nov 2016 11:31:40 GMT :/Users/cr517/Documents/phd/project/STAR/source"' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp

removed

Depend.list clang: warning: parametersDefault.xxd: 'linker' input unused clang: warning: htslib: 'linker' input unused clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' make: * [Depend.list] Error 1

I try to force it to use c++ compiler gcc but it seems it stubbornly uses clang.

Can anyone help me, please?

Thanks.

[GenoMax]

I suggest that you download the pre-compiled binaries for STAR for Mac OS here.

[biomagician]

Thanks, I downloaded it. Can you tell me how to run a command with it, please?

[GenoMax]

Manual for STAR is here.

[biomagician]

Thanks, I made my STAR file executable but I still cannot run any command. The STAR command is not found.

[GenoMax]

To do this ideally you need to amend your $PATH to include the location of STAR directory. Something like (replace path_to with a real path on your system) export PATH=$PATH:/path_to/STAR

[biomagician]

Oh, I forgot to write ./STAR in my command. I was only writing STAR. I think it's working now. Thank you so much.

Answer 1

[Eric Lim]

You should also consider conda and bioconda.

For python3.5 on macos,

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
$ sh Miniconda3-latest-MacOSX-x86_64.sh
# follow on-screen steps to finish installation
$ conda install star -c bioconda

Bioconda is growing steadily and it includes well over 1,500 bioinformatics related packages and frameworks.

[GenoMax]

Does conda always give you the latest version of a program that is available?

[Eric Lim]

Not necessarily. Depends on the package itself. Some have included bioconda as part of the deployment while some depend on community's efforts. But generally speaking, it's pretty updated.