Trinity compile failed

[Kai]

Hi guys,

I got this error message while compiling Trinity:

make[2]: Leaving directory `/home/fengk/pasa/trinityrnaseq-2.2.0/trinity-plugins/htslib'

cd scaffold_iworm_contigs && make

make[2]: Entering directory `/home/fengk/pasa/trinityrnaseq-2.2.0/trinity-plugins/scaffold_iworm_contigs'

g++  -I../htslib -L../htslib ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs

../htslib/libhts.so: undefined reference to `compressBound@ZLIB_1.2.0'

../htslib/libhts.so: undefined reference to `gzungetc@ZLIB_1.2.0.2'

collect2: ld returned 1 exit status

make[2]: *** [ScaffoldIwormContigs] Error 1

make[2]: Leaving directory `/home/fengk/pasa/trinityrnaseq-2.2.0/trinity-plugins/scaffold_iworm_contigs'

make[1]: *** [scaffold_iworm_contigs_target] Error 2

make[1]: Leaving directory `/home/fengk/pasa/trinityrnaseq-2.2.0/trinity-plugins'

make: *** [trinity_essentials] Error 2

What I see here is something wrong while compiling scaffold_iworm_contigs, I am new bioinformatics and have very very limited knowledge to C and C++, so any one can tell me how can I solve this problem?

Thanks,

Kai

[Kai]

forget to mention, my linux distribution is RHEL 6.

在 2016年4月29日星期五 UTC+8下午7:59:20，Kai写道：

[Fulton, Ben]

There appears to be an inconsistency in your system between the zlib header files and the zlib libraries. Are you able to do

 

sudo apt-get install zlib1g-dev

 

Otherwise, simply “make clean” and “make plugins” may fix it.

 

--

Ben Fulton

Research Technologies

Scientific Applications and Performance Tuning

Indiana University

E-Mail: befu...@iu.edu

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[Kai]

well, Ben, thank you for your respond, I did the step make plugins and when I get to the sample_data folder run the runME.sh, I still got errors, has this step any relationship with using Trinity, or I could just ignore this step and use Trinity properly.

Thanks again,

Kai

在 2016年4月29日星期五 UTC+8下午8:41:30，Ben Fulton写道：

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[Fulton, Ben]

It depends on what errors you got. If you had errors with RSEM or eXpress then those don’t affect Trinity – unless of course you need to run RSEM or eXpress later! If you had an error running Trinity in the sample folder then you may have problems running it on your data as well.

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