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Old 09-15-2015, 09:46 AM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 351
Default path error for samtools-1.2 after re-install

I recently re-install ubuntu and am getting a path error, but things seem like they are added.

Code:
cmccabe@HPZ640:~$ echo $PATH
/home/cmccabe/Desktop/ngs_analysis/samtools-1.2/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
cmccabe@HPZ640:~$ cd "/home/cmccabe/Desktop/NGS"
cmccabe@HPZ640:~/Desktop/NGS$ samtools view -H /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam | sed '/^@PG/d' | samtools reheader - /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam > /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam
The program 'samtools' is currently not installed. You can install it by typing:
The program 'samtools' is currently not installed. You can install it by typing:
sudo apt-get install samtools
sudo apt-get install samtools
What am I doing wrong? Thank you .
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Old 09-15-2015, 09:59 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

My samtools is in .../samtools-1.2/bin ... you do not have the 'bin' path in your path thus I suspect that is your problem. Do an

ls /home/cmccabe/Desktop/ngs_analysis/samtools-1.2/

And see what you have there. Then a

ls /home/cmccabe/Desktop/ngs_analysis/samtools-1.2/bin

And see what is there.
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Old 09-15-2015, 10:20 AM   #3
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 351
Default

I do not have a /bin but added the path of where all the binaries are. I am getting a permission denied error and I'm not sure why. Thank you .

Code:
cmccabe@HPZ640:~$ echo $PATH
/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
cmccabe@HPZ640:~$ ls /home/cmccabe/Desktop/NGS/samtools-1.2/
AUTHORS          bam_md.c            bam_tview_html.c  padding.o
bam2bcf.c        bam_md.o            bam_tview_html.o  phase.c
bam2bcf.h        bam.o               bam_tview.o       phase.o
bam2bcf_indel.c  bam_plbuf.c         bedcov.c          README
bam2bcf_indel.o  bam_plbuf.h         bedcov.o          sam.c
bam2bcf.o        bam_plbuf.o         bedidx.c          sam.h
bam2depth.c      bam_plcmd.c         bedidx.o          sam_header.c
bam2depth.o      bam_plcmd.o         ChangeLog.old     sam_header.h
bam_aux.c        bam_reheader.c      cut_target.c      sam_header.o
bam_aux.o        bam_reheader.o      cut_target.o      sam.o
bam.c            bam_rmdup.c         errmod.c          sample.c
bam_cat.c        bam_rmdup.o         errmod.h          sample.h
bam_cat.o        bam_rmdupse.c       errmod.o          sample.o
bam_color.c      bam_rmdupse.o       examples          samtools
bam_color.o      bamshuf.c           faidx.c           samtools.1
bam_endian.h     bamshuf.o           faidx.o           samtools.h
bam_flags.c      bam_sort.c          htslib-1.2.1      sam_view.c
bam_flags.o      bam_sort.o          INSTALL           sam_view.o
bam.h            bam_split.c         kprobaln.c        stats.c
bam_import.c     bam_split.o         kprobaln.h        stats_isize.c
bam_import.o     bam_stat.c          kprobaln.o        stats_isize.h
bam_index.c      bam_stat.o          libbam.a          stats_isize.o
bam_index.o      bamtk.c             LICENSE           stats.o
bam_lpileup.c    bamtk.o             Makefile          test
bam_lpileup.h    bam_tview.c         Makefile.mingw    version.h
bam_lpileup.o    bam_tview_curses.c  misc              win32
bam_mate.c       bam_tview_curses.o  NEWS
bam_mate.o       bam_tview.h         padding.c
cmccabe@HPZ640:~$ ls /home/cmccabe/Desktop/NGS/samtools-1.2/bin
ls: cannot access /home/cmccabe/Desktop/NGS/samtools-1.2/bin: No such file or directory
cmccabe@HPZ640:~$ cd "/home/cmccabe/Desktop/NGS"
cmccabe@HPZ640:~/Desktop/NGS$ samtools view -H /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam | sed '/^@PG/d' | samtools reheader - /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam > /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam
bash: /home/cmccabe/Desktop/NGS/samtools-1.2/samtools: Permission denied
bash: /home/cmccabe/Desktop/NGS/samtools-1.2/samtools: Permission denied
EDIT: forgot to do make install, it's working now. Thank you

Last edited by cmccabe; 09-15-2015 at 10:25 AM.
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