trouble in installing
Closed this issue · 4 comments
huawen-poppy commented
Hello!
when I tried to install the tool, somehow it failed. Could you please help me to fix it? Many thanks!
(base) zhonh0b@kw60822:~/projects/16srrna/kalign-3.3.2$ make
Making all in src
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make all-am
make[2]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[2]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
Making all in dev
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/dev'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/dev'
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2'
(base) zhonh0b@kw60822:~/projects/16srrna/kalign-3.3.2$ make check
Making check in src
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make edist alphabet misc_test bpm_test rwaln rstdin_test
make[2]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[2]: 'alphabet' is up to date.
make[2]: 'misc_test' is up to date.
make[2]: 'bpm_test' is up to date.
make[2]: 'rwaln' is up to date.
make[2]: 'rstdin_test' is up to date.
make[2]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make check-TESTS
make[2]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[3]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
PASS: edist
PASS: alphabet
PASS: misc_test
PASS: bpm_test
PASS: rstdin_test
============================================================================
Testsuite summary for kalign 3.3.2
============================================================================
# TOTAL: 5
# PASS: 5
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[3]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[2]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
Making check in dev
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/dev'
make check-TESTS
make[2]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/dev'
Running kalign basic io test:
a2m.good.1
read/writea2m.good.1 SUCCESS
a2m.good.2
read/writea2m.good.2 SUCCESS
afa.good.1
read/writeafa.good.1 SUCCESS
afa.good.2
read/writeafa.good.2 SUCCESS
afa.good.3
read/writeafa.good.3 SUCCESS
clustal.good.1
read/writeclustal.good.1 SUCCESS
clustal.good.2
read/writeclustal.good.2 SUCCESS
PASS: run_io_test.sh
Running kalign basic alignment tests:
BB11001.msf
read/writeBB11001.msf SUCCESS
BB11001_EOF.msf
read/writeBB11001_EOF.msf SUCCESS
BB11001.tfa
read/writeBB11001.tfa SUCCESS
BB12006.msf
read/writeBB12006.msf SUCCESS
BB12006.tfa
read/writeBB12006.tfa SUCCESS
BB30014.msf
read/writeBB30014.msf SUCCESS
BB30014.tfa
read/writeBB30014.tfa SUCCESS
PASS: run_aln_test.sh
==================
All 2 tests passed
==================
make[2]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/dev'
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/dev'
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2'
make[1]: Nothing to be done for 'check-am'.
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2'
(base) zhonh0b@kw60822:~/projects/16srrna/kalign-3.3.2$ make install
Making install in src
make[1]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
make[2]: Entering directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
/bin/mkdir -p '/usr/local/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c kalign kchaos '/usr/local/bin'
libtool: install: /usr/bin/install -c kalign /usr/local/bin/kalign
/usr/bin/install: cannot create regular file '/usr/local/bin/kalign': Permission denied
Makefile:823: recipe for target 'install-binPROGRAMS' failed
make[2]: *** [install-binPROGRAMS] Error 1
make[2]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
Makefile:1597: recipe for target 'install-am' failed
make[1]: *** [install-am] Error 2
make[1]: Leaving directory '/home/zhonh0b/projects/16srrna/kalign-3.3.2/src'
Makefile:413: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1
TimoLassmann commented
Hi, it seems you do not have administrator/root permissions on your machine (the clue is here: cannot create regular file '/usr/local/bin/kalign': Permission denied).
You could just create a ~/bin directory in your home directory, copy the kalign executable there and add this to your PATH variable.
huawen-poppy commented
Thank you for your quick reply!
I tried the suggestion you gave, somehow still failed.
(base) [zhonh0b@login509-02-r bin]$ cd kalign/
(base) [zhonh0b@login509-02-r kalign]$ ls
AUTHORS INSTALL Makefile.in README.md autogen.sh config.log configure dev libtool missing test-driver
COPYING Makefile NEWS VERSION autom4te.cache config.status configure.ac doc ltmain.sh scripts version.sh
ChangeLog Makefile.am README aclocal.m4 config.guess config.sub depcomp install-sh m4 src
(base) [zhonh0b@login509-02-r kalign]$ pwd
/home/zhonh0b/bin/kalign
(base) [zhonh0b@login509-02-r kalign]$ export PATH=$PATH:/home/zhonh0b/bin/kalign/
(base) [zhonh0b@login509-02-r kalign]$ kalign -help
-bash: kalign: command not found
(base) [zhonh0b@login509-02-r kalign]$ kalign -h
-bash: kalign: command not found
TimoLassmann commented
Hi,
The kalign executable is in ~/bin/kalign/src and your PATH variable points to ~/bin/kalign.
What you should do is compile kalign somewhere, let's say ~/programs/kalign , then:
1) cp ~/programs/kalign/src/kalign ~/bin
2) export PATH=/home/zhonh0b/bin:$PATH
Note that in the line above the bin directory in your home directory appears first. This ensures that the programs you install there will be executed in favour of programs installed system wide.
huawen-poppy commented
Geat! Thank you very much for the detailed instructions! It works!