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Old 06-28-2013, 05:27 PM   #1
jazz
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Default libgtextutils installation problem for FASTX toolkit

I am trying to install libgtextutils for running the FASTX toolkit on my Ubuntu, but I am getting the following error after 'sudo make install' command

Making install in m4
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/aclocal" || /bin/mkdir -p "/usr/share/aclocal"
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
Making install in src
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
Making install in gtextutils
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[3]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
test -z "/usr/lib" || /bin/mkdir -p "/usr/lib"
/bin/bash ../../libtool --mode=install /usr/bin/install -c 'libgtextutils.la' '/usr/lib/libgtextutils.la'
libtool: install: /usr/bin/install -c .libs/libgtextutils-0.6.1.so.0.0.0 /usr/lib/libgtextutils-0.6.1.so.0.0.0
/usr/bin/install: cannot stat `.libs/libgtextutils-0.6.1.so.0.0.0': No such file or directory
make[3]: *** [install-libLTLIBRARIES] Error 1
make[3]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
make: *** [install-recursive] Error 1

Can anyone help me in this, since this tool is crucial for running FASTX.

thanks
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Old 06-28-2013, 05:31 PM   #2
jazz
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After a 'make check' I get the following error

jkhurana@jkhurana-ThinkPad-T530:~/Downloads/libgtextutils-0.6.1$ make check
Making check in m4
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
Making check in src
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
Making check in gtextutils
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
Making check in doc
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/doc'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/doc'
Making check in tests
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/tests'
make test_container_join test_natural_sort test_input_stream_wrapper test_text_reader test_text_reader_unget test_fd_outbuf test_fd_inbuf test_in_out_buf test_pipe_fitter test_string_tokenize
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/tests'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT test_container_join.o -MD -MP -MF .deps/test_container_join.Tpo -c -o test_container_join.o test_container_join.cpp
mv -f .deps/test_container_join.Tpo .deps/test_container_join.Po
/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -o test_container_join test_container_join.o ../src/gtextutils/libgtextutils.la
libtool: link: g++ -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -o .libs/test_container_join test_container_join.o ../src/gtextutils/.libs/libgtextutils.so
g++: error: ../src/gtextutils/.libs/libgtextutils.so: No such file or directory
make[2]: *** [test_container_join] Error 1
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/tests'
make: *** [check-recursive] Error 1
jkhurana@jkhurana-ThinkPad-T530:~/Downloads/libgtextutils-0.6.1$
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Old 06-28-2013, 06:03 PM   #3
jazz
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never mind, I solved it!
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Old 07-17-2013, 10:31 AM   #4
nareshvasani
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Default How did you install and run fastx toolkit in linux

Hi,

I am new to NGS data analysis.
Can you please tell me how you installed and run the fastx toolkit in linux.
I would greatly appreciate your help.

Thanks
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Old 07-17-2013, 11:20 AM   #5
GenoMax
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Quote:
Originally Posted by nareshvasani View Post
Hi,

I am new to NGS data analysis.
Can you please tell me how you installed and run the fastx toolkit in linux.
I would greatly appreciate your help.

Thanks
The install instructions are on the download page: http://hannonlab.cshl.edu/fastx_toolkit/download.html

What OS are you using (or are planning to use)?
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Old 07-17-2013, 11:33 AM   #6
nareshvasani
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I also follow same protocol for installation.
I am using linux 64.

After typing
make
message apperas like: make: *** No targets specified and no makefile found. Stop.

After typing
sudo make install
message apperas like: make: *** No rule to make target `install'. Stop.

Can you please explain what does this mean.

Thanks
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Old 07-17-2013, 11:37 AM   #7
GenoMax
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If you downloaded a pre-compiled binary (e.g. from here http://hannonlab.cshl.edu/fastx_tool..._amd64.tar.bz2) then there is nothing more to do (except unzip the file, of course). The program is ready for use.

If you are new to unix then getting the pre-compiled binaries may be the best option.

Are you using Ubuntu?
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Old 07-17-2013, 11:45 AM   #8
nareshvasani
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Thanks for your feedback.

Yes I am using Ubuntu and I downloaded same version.
I was just confused if i install it properly or not.
Is there any command line by which I can assure if the program is installled correctly or not?

Thanks... GenoMax
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Old 07-17-2013, 11:51 AM   #9
GenoMax
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Once you "bunzip2" the file it should make a directory with the name "bin". The fastx toolkit executables will be in that directory. You can change to the bin directory and then try to run of of the files like this:

Code:
$ fastx_trimmer -h
That should produce some help output for the command.

In that case you are all set.
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Old 07-17-2013, 12:05 PM   #10
nareshvasani
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Thanks a lot Genomax.
With your help I am satisfied that I have install program in correct manner.
I appreciate that.

By any chance do you know how to install trinity?

Best,
Naresh
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Old 07-17-2013, 12:11 PM   #11
GenoMax
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Quote:
Originally Posted by nareshvasani View Post
Thanks a lot Genomax.
With your help I am satisfied that I have install program in correct manner.
I appreciate that.

By any chance do you know how to install trinity?

Best,
Naresh
Follow the directions on the trinity page (it is a "make" provided you have the dependencies).

There are a couple of threads that may help, if you run into problems:

http://seqanswers.com/forums/showthread.php?t=31187
http://seqanswers.com/forums/showthread.php?t=31661

If you get errors post them here.
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Old 07-17-2013, 12:30 PM   #12
nareshvasani
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Much Appreciated Genomax.

make commond means it helps to update files correct?
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Old 07-17-2013, 03:02 PM   #13
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Quote:
Originally Posted by nareshvasani View Post
make commond means it helps to update files correct?
Quote:
Make is a utility that automatically builds executable programs and libraries from source code by reading files called makefiles which specify how to derive the target program.
From: http://en.wikipedia.org/wiki/Make_%28software%29
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Old 07-18-2013, 06:53 AM   #14
nareshvasani
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Thanks GenoMax
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Old 07-18-2013, 07:18 AM   #15
nareshvasani
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Smile libgtextutils-0.6 installation problem

Trying to install libgtextutils-0.6

After make coomand
below message pop up

[root@Victor-20 libgtextutils-0.6]# make
make all-recursive
make[1]: Entering directory `/root/libgtextutils-0.6'
Making all in m4
make[2]: Entering directory `/root/libgtextutils-0.6/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/root/libgtextutils-0.6/m4'
Making all in src
make[2]: Entering directory `/root/libgtextutils-0.6/src'
Making all in gtextutils
make[3]: Entering directory `/root/libgtextutils-0.6/src/gtextutils'
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c -o pipe_fitter.lo pipe_fitter.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c pipe_fitter.c -fPIC -DPIC -o .libs/pipe_fitter.o
pipe_fitter.c: In function ‘pipe_close’:
pipe_fitter.c:30:6: error: variable ‘i’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[3]: *** [pipe_fitter.lo] Error 1
make[3]: Leaving directory `/root/libgtextutils-0.6/src/gtextutils'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/libgtextutils-0.6/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/libgtextutils-0.6'
make: *** [all] Error 2

Can you please help me out to solve this issue

Thanks,
Naresh
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Old 07-18-2013, 11:01 AM   #16
GenoMax
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Why don't you install the library either by using Ubuntu software center/method below?

Code:
$sudo apt-get install libgtextutils0
Since you got the precompiled binaries for fastx-toolkit you should not need to install this separately.
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Old 07-18-2013, 11:16 AM   #17
nareshvasani
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Thanks GenoMax.
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Old 02-27-2014, 01:26 AM   #18
Zhang Siting
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Question make errors

I have met the same problem. How to solve it? Anybody helps?
Quote:
Originally Posted by jazz View Post
I am trying to install libgtextutils for running the FASTX toolkit on my Ubuntu, but I am getting the following error after 'sudo make install' command

Making install in m4
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/aclocal" || /bin/mkdir -p "/usr/share/aclocal"
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
Making install in src
make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
Making install in gtextutils
make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[3]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
test -z "/usr/lib" || /bin/mkdir -p "/usr/lib"
/bin/bash ../../libtool --mode=install /usr/bin/install -c 'libgtextutils.la' '/usr/lib/libgtextutils.la'
libtool: install: /usr/bin/install -c .libs/libgtextutils-0.6.1.so.0.0.0 /usr/lib/libgtextutils-0.6.1.so.0.0.0
/usr/bin/install: cannot stat `.libs/libgtextutils-0.6.1.so.0.0.0': No such file or directory
make[3]: *** [install-libLTLIBRARIES] Error 1
make[3]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
make: *** [install-recursive] Error 1

Can anyone help me in this, since this tool is crucial for running FASTX.

thanks
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Old 02-27-2014, 05:47 AM   #19
nareshvasani
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Quote:
Originally Posted by Zhang Siting View Post
I have met the same problem. How to solve it? Anybody helps?
Install the library either by using Ubuntu software center/method below:

Code:
$sudo apt-get install libgtextutils0

Best,
Naresh
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Old 02-28-2014, 03:35 AM   #20
Zhang Siting
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Default Problem solved

, thanks for your quick reply.
This method doesn't work for me anyway. But I solve the problem just using the latest version of libgtextutils and fastx-toolkit. Hope this info helps.

Quote:
Originally Posted by nareshvasani View Post
Install the library either by using Ubuntu software center/method below:

Code:
$sudo apt-get install libgtextutils0

Best,
Naresh
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