Question: Help with Fastq-Tools Install
0
gravatar for landrjos
6 days ago by
landrjos0
landrjos0 wrote:

Hi All,

I am trying to install fasts-tools. I have successfully installed pcre2 and libc but cant install fasts-tools build 8. This is the error I am getting. Can anyone give a suggestion as to what I am doing wrong?

Making install in src
  CC       common.o
  CCLD     fastq-grep
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-kmers
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-match
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-uniq
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-qual
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-sample
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-qualadj
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-sort
../libtool: line 7899: func_munge_path_list: command not found
  CCLD     fastq-qscale
../libtool: line 7899: func_munge_path_list: command not found
 .././install-sh -c -d '/usr/local/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c fastq-grep fastq-kmers fastq-match fastq-uniq fastq-qual fastq-sample fastq-qualadj fastq-sort fastq-qscale '/usr/local/bin'
libtool: install: /usr/bin/install -c fastq-grep /usr/local/bin/fastq-grep
install: /usr/local/bin/fastq-grep: Permission denied
make[2]: *** [install-binPROGRAMS] Error 71
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1
SOMGEGRL01134EM:fastq-tools-0.8 jwlandry2$

Thanks,

Jos

ADD COMMENTlink modified 6 days ago by Kevin Blighe6.6k • written 6 days ago by landrjos0

Is this your own computer? Looks like you don't have permissions to install globally.

ADD REPLYlink written 6 days ago by st.ph.n1.9k

This is a university computer. What do I need the IT people to do?

ADD REPLYlink written 6 days ago by landrjos0

You can install locally to your home folder. Check the README, or program manual for the software. If there's a configure script, typically one can use --prefix to provide the install path, prior to running make install. As is a university computer, check with someone first. If it is a lab server, check with the PI or lab assistants.

ADD REPLYlink modified 6 days ago • written 6 days ago by st.ph.n1.9k

The problem we are having is that the fasts-tools does not come with a readme file. There are no install instructions at all.

Would the install path be in the program folder /Users/jwlandry2/Desktop/Bioinfor.Tools/fastq-tools-0.8?

here are the contents of the fastq-tools folder. AUTHORS TODO config.status doc missing COPYING aclocal.m4 config.sub install-sh src Makefile compile configure libtool test-driver Makefile.am config.guess configure.ac ltmain.sh tests Makefile.in config.log depcomp m4

What would be the commands I would use to do the install? I tried...

SOMGEGRL01134EM:fastq-tools-0.8 jwlandry2$ ./configure && make install

and that gave me the error.

ADD REPLYlink written 6 days ago by landrjos0

You should not need to strictly install them. After you get them compiled, use them from whatever directory they are in by appending it to your $PATH or copying the executables to a directory already present in your $PATH. You could also look into the --prefix method mentioned above.

ADD REPLYlink modified 6 days ago • written 6 days ago by genomax37k

Hi, I'm the I.T. analyst working to help get this installed.

What should we be logged in as exactly? You stated we cannot install globally, but I'm the admin on this machine. By globally, what exactly do you mean? Are you saying we need superuser privileges?

ADD REPLYlink written 6 days ago by landrjos0

Correct. To install in /use/local/bin you would need elevated privileges. If you have sudo access then for the make install part you can use sudo make install. Otherwise you may need to log in as root for the make install part.

ADD REPLYlink modified 6 days ago • written 6 days ago by genomax37k
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