Unable to find '_BINDIR_/pstacks' when running ref_map.pl

[A. G-E]

Hello stack users, 

I am trying to run the ref_map.pl program and am running into this error:  Unable to find '_BINDIR_/pstacks'

I followed the instructions on a previous thread (https://groups.google.com/forum/#!topic/stacks-users/plg5pyFCwIk) but am still getting this error. I added the program to my PATH. 

Any idea what could be causing it? 

e.g. 

ref_map.pl -m 4 -T 14 -b 1 -S --samples ./Volumes/WFMQUEBEC/pero_sam/samfiles -o ./stacks07nov16/ -O ./Volumes/WFMQUEBEC/pero_sam/samfiles/popmap.txt  -X "populations:--max_obs_het 0.75" -X "populations:--vcf" -X "populations:--plink" -X "populations:--genepop" -X "populations:--structure" -X "populations:--write_random_snp" -X "populations:--fstats"

Unable to find '_BINDIR_/pstacks'.

Thanks,

Alan

[Nicolas Rochette]

Hi Alan,

_BINDIR_ is normally replaced with the actual directory at the end of the installation process. Have you run `make install` ?

Best,

Nicolas

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[A. G-E]

Hi Nicolas,

Thank you for your reply. 

I did run the three commands "./configure, ./make, ./make install" and I still get the same error. 

After the make install command I get this:

Making install in htslib

make[1]: Nothing to be done for `install'.

Making install in .

 config/install-sh -c -d '/usr/local/bin'

  /usr/bin/install -c ustacks pstacks estacks cstacks sstacks rxstacks hstacks process_radtags process_shortreads kmer_filter clone_filter genotypes populations phasedstacks '/usr/local/bin'

install: /usr/local/bin/ustacks: Permission denied

make[2]: *** [install-binPROGRAMS] Error 71

make[1]: *** [install-am] Error 2

make: *** [install-recursive] Error 1

I'm trying to run it on an external HD so I'm not sure if that would affect it.

Alan

[Nicolas Rochette]

Hi Alan,

The install failed ("Error", "Permission denied", etc.) because you need to specify where you want to install Stacks. You can use either sudo or configure's --prefix option. Please refer to the manual: http://catchenlab.life.illinois.edu/stacks/manual/#install

Best,

Nicolas

A. G-E wrote on 12/05/2016 04:39 PM:

[A. G-E]

Hi Nicolas,

Thanks for your reply. I've read the manual multiple times but unfortunately it still doesn't work. 

I added and extracted the stacks file in my external drive (/VOLUMES). 

then: 

$ ./configure --prefix=/VOLUMES

$ make 

Unable to find '_BINDIR_/pstacks'.

(make install gave errors: make[1]: Nothing to be done for `install' and sudo make install asked for a password I didn't know)

Is that not the right way to do it? 

I apologize for such trivial issue. I previously ran the pipeline with v.1.37 and had no problem but I deleted that version. 

Thanks, 

Alan

[A. G-E]

Nevermind, it works when I run pstacks on its own. 

Thanks,

Alan

[A. G-E]

Hello, 

I tried the ./configure --prefix/path/to/stacks-4.11 

 make install resulted in  No rule to make target `install'.  Stop.

sudo make install asks for password (I'm  using a cluster and did't have the permission)

make is the only one that worked for me. 

What worked solved the _BINDIR_ error (so far no error):

move all programs  from scripts (e.g. ref_map.pl) directory to the main stacks one. 

Open ref_map.pl and change the exec_path  from '_BINDIR_'  to 'path/to/stacksdirectory'

Then change the permission: chmod 777 ref_map.pl  

This seems to be working.  I hope it helps others.

Alan