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Old 07-24-2013, 04:55 PM   #1
LVAndrews
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Location: Flagstaff, AZ

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Default lastz and yasra install problems

Hello,

I am attempting to install lastz and yasra for plastid genome assembly, but am having problems. I downloaded lastz here:

http://www.bx.psu.edu/~rsharris/lastz/

and yasra v1 here:

http://www.bx.psu.edu/~ratan/archive/

I was informed by the user that they needed yasra v1 as later versions are not compatible with their pipeline. Anyway, I downloaded yasra first, but it didn't want to install, so I moved on to lastz. I issued:

sudo make

which produced some errors. I googled a bit, and found a thread here on seqanswers where it was suggested to go into the lastz makefile, and delete -Werror from line 31, and repeat install. It worked!

But then I tried to install yasra and it seems it is dependent on -Werror:

sudo make
make pipeline
make[1]: Entering directory `/bin/yasra'
gcc -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror -Wno-unused-variable -Wunused-parameter -Wreturn-type -Wpointer-arith -Wswitch -Wcast-align -Winline -Wnested-externs -Wextra -DNDEBUG -O2 -funroll-all-loops -minline-all-stringops -momit-leaf-frame-pointer -I. -c -o substitutions.o substitutions.c
substitutions.c: In function ‘main’:
substitutions.c:35:52: error: variable ‘match’ set but not used [-Werror=unused-but-set-variable]
substitutions.c:34:7: error: variable ‘old_seq_name’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[1]: *** [substitutions.o] Error 1
make[1]: Leaving directory `/bin/yasra'
make: *** [all] Error 2

I am doing all of this in my /bin directory since I can't seem to get new directories added permanently to my path (I only seem to know enough to cause trouble for myself and others), which is why I am using sudo with each command. I thought perhaps directory permissions were really the cause of my trouble, so I moved the lastz folder to my desktop and repeated the make command, but got the same problem output:

sudo make
cd src && make lastz lastz_D
make[1]: Entering directory `/home/enggen/Downloads/lastz-distrib-1.02.00/src'
gcc -c -O3 -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DVERSION_MAJOR="\"1"\" -DVERSION_MINOR="\"02"\" -DVERSION_SUBMINOR="\"00"\" -DREVISION_DATE="\"20100112"\" -DSUBVERSION_REV="\"1278:1279M"\" -Dscore_type=\'I\' lastz.c -o lastz.o
lastz.c: In function ‘main’:
lastz.c:441:9: error: variable ‘freeTargetRev’ set but not used [-Werror=unused-but-set-variable]
lastz.c: In function ‘start_one_strand’:
lastz.c:1669:9: error: variable ‘base****’ set but not used [-Werror=unused-but-set-variable]
lastz.c: In function ‘parse_options’:
lastz.c:5048:9: error: variable ‘seq1Filename’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[1]: *** [lastz.o] Error 1
make[1]: Leaving directory `/home/enggen/Downloads/lastz-distrib-1.02.00/src'
make: *** [build_lastz] Error 2

I am running 64bit Ubuntu 12.04, which may or may not place certain files in the same place as other linux distros.

Any ideas how to solve these problems?
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Old 01-20-2014, 01:38 AM   #2
amitbik
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Default lastz problem

same here also...

Did any you find the solution??

Thanks...
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Old 01-20-2014, 02:33 AM   #3
amitbik
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Default

i got the answer. it is actually posted by scami

1) Open the Makefile file within the src directory with a text editor
2) Delete the word -Werror at the line 31 . Save and quit
3) Repeat the make / make install procedure

By follwing this step i got the executable file.
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Old 01-20-2014, 08:18 AM   #4
LVAndrews
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Default

I thought I had tried that previously, but the user went and tried the free version of Geneious and used that instead (pretty great assembler). Their lab wound up purchasing a license as did we. If I have future need for yasra/lastz, I'll give these instructions a try.
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Old 07-13-2014, 09:35 AM   #5
Topulaneus-Hattum
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Default

Quote:
Originally Posted by AKrohn View Post
Hello,
(I only seem to know enough to cause trouble for myself and others), which is why I am using sudo with each command.
This is why there are such things as botnets.
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