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install of STAR

Hello,

I downloaded the STAR-2.6.0a from https://github.com/alexdobin/STAR/releases, following the file README.md. It looks has compiled.

cd STAR/source
make STAR

When I ran this program, it said command not found.

Thank in advance for great help!

Yue

root@ACB-HuangLab-Ubuntu:/media/administrator/DATA/STAR-2.6.0a/source# STAR
STAR:未找到命令

root@ACB-HuangLab-Ubuntu:/media/administrator/DATA/STAR-2.6.0a/source# ls
alignSmithWaterman.cpp                       genomeParametersWrite.cpp                 ReadAlignChunk.cpp                          sjdbInsertJunctions.o
alignSmithWaterman.h                         genomeParametersWrite.h                   ReadAlignChunk.h                            sjdbLoadFromFiles.cpp
alignSmithWaterman.o                         genomeParametersWrite.o                   ReadAlignChunk_mapChunk.cpp                 sjdbLoadFromFiles.h
BAMbinSortByCoordinate.cpp                   genomeSAindex.cpp                         ReadAlignChunk_mapChunk.o                   sjdbLoadFromFiles.o
BAMbinSortByCoordinate.h                     genomeSAindex.h                           ReadAlignChunk.o                            sjdbLoadFromStream.cpp
BAMbinSortByCoordinate.o                     genomeSAindex.o                           ReadAlignChunk_processChunks.cpp            sjdbLoadFromStream.h
BAMbinSortUnmapped.cpp                       genomeScanFastaFiles.cpp                  ReadAlignChunk_processChunks.o              sjdbLoadFromStream.o
BAMbinSortUnmapped.h                         genomeScanFastaFiles.h                    ReadAlign_CIGAR.cpp                         sjdbPrepare.cpp
BAMbinSortUnmapped.o                         genomeScanFastaFiles.o                    ReadAlign.cpp                               sjdbPrepare.h
bam_cat.c                                    GlobalVariables.cpp                       ReadAlign_createExtendWindowsWithAlign.cpp  sjdbPrepare.o
bam_cat.h                                    GlobalVariables.h                         ReadAlign_createExtendWindowsWithAlign.o    sortSuffixesBucket.h
bam_cat.o                                    hg38.fa                                   ReadAlign.h                                 STAR
BAMfunctions.cpp                             Homo_sapiens.GRCh38.83.gtf                ReadAlign_mapOneRead.cpp                    STAR.cpp
BAMfunctions.h                               htslib                                    ReadAlign_mapOneRead.o                      STAR.o
BAMfunctions.o                               IncludeDefine.h                           ReadAlign_mappedFilter.cpp                  Stats.cpp
BA
rna-seq

Hello yueli7!

We believe that this post does not fit the main topic of this site.

just a PATH problem https://opensource.com/article/17/6/set-path-linux "Telling your Linux shell where to look for executable files is easy, and something everyone should be able to do."

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

1 answer

It does appear that STAR has been compiled. You would want to add this directory to your $PATH to make STAR seamlessley available. You can do export PATH=$PATH:/the_dir_with_STAR. Otherwise run it as ./STAR -h.

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