TRINITY tool installation help

Question

[iamtuttu5]

Hi everyone,

I was trying to run Trinity tool for assembly of plant RNA data. I am running it on a ubuntu server through putty. But it results in following errorr while I was trying to make the trinity file (compilation terminated in between). I am just a beginner in linux , anyone please help me on this regard.

Error obtained:

tuttu@kau:~/ngs/trinityrnaseq-2.1.1$ sudo make
[sudo] password for tuttu:
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
                && sh ./configure --prefix=`pwd`  && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory `/home/jinu/ngs/trinityrnaseq-2.1.1/Inchworm'
Making install in src
make[2]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
make[3]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
test -z "/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/bin" || /bin/mkdir -p "/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/bin"
  /usr/bin/install -c inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats '/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
make[2]: Leaving directory `/home/tutu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
make[2]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[3]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[2]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[1]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
cd Chrysalis && make UNSUPPORTED=yes
make[1]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Chrysalis'
make[1]: Nothing to be done for `all'.tu
make[1]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Chrysalis'
cd trinity-plugins && make trinity_essentials
make[1]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins'
tar xvf "htslib.github.Aug182015.tar.gz" && cd htslib && make
htslib/
htslib/tbx.c
htslib/README.md
htslib/htsfile.1
htslib/config.h.in
htslib/LICENSE
htslib/htslib/
htslib/htslib/khash_str2int.h
htslib/htslib/kfunc.h
htslib/htslib/faidx.h
htslib/htslib/khash.h
htslib/htslib/ksort.h
htslib/htslib/tbx.h
htslib/htslib/vcf.h
htslib/htslib/regidx.h
htslib/htslib/hts.h
htslib/htslib/hfile.h
htslib/htslib/vcfutils.h
htslib/htslib/synced_bcf_reader.h
htslib/htslib/hts_defs.h
htslib/htslib/kstring.h
htslib/htslib/kseq.h
htslib/htslib/vcf_sweep.h
htslib/htslib/knetfile.h
htslib/htslib/sam.h
htslib/htslib/klist.h
htslib/htslib/cram.h
htslib/htslib/bgzf.h
htslib/hfile_irods.c
htslib/htslib.pc.in
htslib/htslib_vars.mk
htslib/test/
htslib/test/c1.fa.fai
htslib/test/xx#minimal.sam
htslib/test/c1#noseq.sam
htslib/test/ce.fa
htslib/test/c1.fa
htslib/test/ce#unmap2.sam
htslib/test/ce#2.sam
htslib/test/test-vcf-api.out
htslib/test/ce#5b.sam
htslib/test/xx#tlen.sam
htslib/test/test-vcf-api.c
htslib/test/ce#1.sam
htslib/test/test-regidx.c
htslib/test/xx#tlen2.sam
htslib/test/ce#unmap.sam
htslib/test/sam.c
htslib/test/c1#pad3.sam
htslib/test/c1#pad1.sam
htslib/test/ce#large_seq.sam
htslib/test/test_view.pl
htslib/test/c2.fa.fai
htslib/test/c1#pad2.sam
htslib/test/xx#unsorted.sam
htslib/test/ce#5.sam
htslib/test/c1#clip.sam
htslib/test/xx#large_aux.sam
htslib/test/xx#blank.sam
htslib/test/c1#bounds.sam
htslib/test/ce#tag_padded.sam
htslib/test/hfile.c
htslib/test/xx#pair.sam
htslib/test/ce#tag_depadded.sam
htslib/test/xx#rg.sam
htslib/test/test.pl
htslib/test/xx.fa
htslib/test/auxf#values.sam
htslib/test/xx#triplet.sam
htslib/test/compare_sam.pl
htslib/test/xx#large_aux2.sam
htslib/test/cross_validate.sh
htslib/test/ce#unmap1.sam
htslib/test/xx.fa.fai
htslib/test/auxf.fa
htslib/test/test-vcf-sweep.out
htslib/test/c2.fa
htslib/test/fieldarith.c
htslib/test/ce.fa.fai
htslib/test/c2#pad.sam
htslib/test/ce#supp.sam
htslib/test/test-vcf-sweep.c
htslib/test/test_view.c
htslib/test/fieldarith.sam
htslib/test/auxf.fa.fai
htslib/test/c1#unknown.sam
htslib/sam.c
htslib/INSTALL
htslib/hfile_net.c
htslib/configure.ac
htslib/tabix.c
htslib/sam.5
htslib/cram/
htslib/cram/cram_io.h
htslib/cram/open_trace_file.h
htslib/cram/thread_pool.c
htslib/cram/zfio.c
htslib/cram/zfio.h
htslib/cram/string_alloc.h
htslib/cram/vlen.c
htslib/cram/rANS_byte.h
htslib/cram/mFILE.c
htslib/cram/cram_encode.c
htslib/cram/cram_codecs.h
htslib/cram/cram_external.c
htslib/cram/string_alloc.c
htslib/cram/rANS_static.c
htslib/cram/open_trace_file.c
htslib/cram/files.c
htslib/cram/cram_samtools.h
htslib/cram/rANS_static.h
htslib/cram/sam_header.c
htslib/cram/cram_structs.h
htslib/cram/cram_index.c
htslib/cram/cram_decode.c
htslib/cram/pooled_alloc.h
htslib/cram/mFILE.h
htslib/cram/cram_stats.h
htslib/cram/os.h
htslib/cram/pooled_alloc.c
htslib/cram/cram_encode.h
htslib/cram/cram_index.h
htslib/cram/cram_stats.c
htslib/cram/cram_codecs.c
htslib/cram/vlen.h
htslib/cram/cram_samtools.c
htslib/cram/cram_decode.h
htslib/cram/sam_header.h
htslib/cram/thread_pool.h
htslib/cram/misc.h
htslib/cram/cram.h
htslib/cram/cram_io.c
htslib/Makefile
htslib/hfile.c
htslib/README
htslib/knetfile.c
htslib/bgzf.c
htslib/faidx.c
htslib/vcf.c
htslib/kstring.c
htslib/synced_bcf_reader.c
htslib/bgzip.c
htslib/hts_internal.h
htslib/.gitignore
htslib/hts.c
htslib/tabix.1
htslib/config.mk.in
htslib/hfile_internal.h
htslib/.git/
htslib/.git/branches/
htslib/.git/packed-refs
htslib/.git/HEAD
htslib/.git/description
htslib/.git/info/
htslib/.git/info/exclude
htslib/.git/refs/
htslib/.git/refs/heads/
htslib/.git/refs/heads/develop
htslib/.git/refs/remotes/
htslib/.git/refs/remotes/origin/
htslib/.git/refs/remotes/origin/cram_index_fix454
htslib/.git/refs/remotes/origin/HEAD
htslib/.git/refs/remotes/origin/develop
htslib/.git/refs/tags/
htslib/.git/FETCH_HEAD
htslib/.git/index
htslib/.git/logs/
htslib/.git/logs/HEAD
htslib/.git/logs/refs/
htslib/.git/logs/refs/heads/
htslib/.git/logs/refs/heads/develop
htslib/.git/logs/refs/remotes/
htslib/.git/logs/refs/remotes/origin/
htslib/.git/logs/refs/remotes/origin/cram_index_fix454
htslib/.git/logs/refs/remotes/origin/HEAD
htslib/.git/logs/refs/remotes/origin/develop
htslib/.git/config
htslib/.git/hooks/
htslib/.git/hooks/update.sample
htslib/.git/hooks/pre-commit.sample
htslib/.git/hooks/pre-push.sample
htslib/.git/hooks/applypatch-msg.sample
htslib/.git/hooks/pre-applypatch.sample
htslib/.git/hooks/post-update.sample
htslib/.git/hooks/pre-rebase.sample
htslib/.git/hooks/commit-msg.sample
htslib/.git/hooks/prepare-commit-msg.sample
htslib/.git/ORIG_HEAD
htslib/.git/objects/
htslib/.git/objects/c4/
htslib/.git/objects/c4/dcd9310892b5d6ce73bd4d432f2cdb5d185b86
htslib/.git/objects/d7/
htslib/.git/objects/d7/5415141386bd7af4a3b0c18ce9c72b58c0895e
htslib/.git/objects/f7/
htslib/.git/objects/f7/9045536b9bb89666bedf7ee665503a0d9bad2a
htslib/.git/objects/d0/
htslib/.git/objects/d0/4c125779fc55599e27217ea16bfa81eb329ce0
htslib/.git/objects/77/
htslib/.git/objects/77/e93b8f53693557080d7eb7dc819f81ec02364e
htslib/.git/objects/77/8653c5935e1a7ded2305db8eb8d9b2b027f6d5
htslib/.git/objects/a5/
htslib/.git/objects/a5/25f1dcd387ed9c498651d9ca52f7f2b3f7cbd2
htslib/.git/objects/35/
htslib/.git/objects/35/aa79fce8592f9fb6b9cc398035e8d3b8f61216
htslib/.git/objects/pack/
htslib/.git/objects/pack/pack-8b94c94d585cec4f62afce453de1b8cc15451ed0.idx
htslib/.git/objects/pack/pack-8b94c94d585cec4f62afce453de1b8cc15451ed0.pack
htslib/.git/objects/c7/
htslib/.git/objects/c7/54ea68af5c2b729639f4c900c53e5e4096e736
htslib/.git/objects/81/
htslib/.git/objects/81/e6a04ea0d63e72eb80b704e4bef9d7c602097c
htslib/.git/objects/9e/
htslib/.git/objects/9e/62c629a55841a79ef98d70329cd19d3ab6e7b2
htslib/.git/objects/44/
htslib/.git/objects/44/94fa66822f0fad7f9715ed6925939295f3e87a
htslib/.git/objects/44/128b6e6d073f5026b6ad1b19309e35607fd06b
htslib/.git/objects/7e/
htslib/.git/objects/7e/a4c18f0f50926e0105ea9e5a42accf5ff5f7ff
htslib/.git/objects/7e/2fbe7367128cdc23ba86bee51734d76933146a
htslib/.git/objects/b8/
htslib/.git/objects/b8/59b9b01afc995480fb5308f04598982f677009
htslib/.git/objects/6f/
htslib/.git/objects/6f/68c606364c438a4d176acc5d7b664468e7d472
htslib/.git/objects/info/
htslib/.git/objects/23/
htslib/.git/objects/23/ba31e625abe185d3d1e46e911f9c8fd8a0963b
htslib/.git/objects/d1/
htslib/.git/objects/d1/aedf5ce3686ec0bc2b7295a8995643a3340e2b
htslib/.git/objects/8c/
htslib/.git/objects/8c/2d8ff9cd4673bf397b6281a77514caa00c5735
htslib/.git/objects/88/
htslib/.git/objects/88/72c10996c6789c25b96dab9ef037da1d1da685
htslib/.git/objects/ee/
htslib/.git/objects/ee/a7813f8c37eb34d09582a12834b448ce18eed7
htslib/.git/objects/fe/
htslib/.git/objects/fe/fcbcabcbd770ab3fa8c20aeb3ae1769824c8d1
htslib/.git/objects/28/
htslib/.git/objects/28/616da42f9f07650a279e07c887ece24cf2b3f4
htslib/.git/objects/13/
htslib/.git/objects/13/b38fb0a3127ae1ec555ca1fd722004a7dba0af
htslib/.git/objects/c9/
htslib/.git/objects/c9/ce386ad3a01d0bb2df4cad26f0f377feead353
htslib/.git/objects/73/
htslib/.git/objects/73/2a5763f9bfeea52ff21b5238334786e5cc3e6a
htslib/.git/objects/45/
htslib/.git/objects/45/baa0e2c299aff7b5934d31c62431348b372174
htslib/.git/objects/7f/
htslib/.git/objects/7f/323b8eac960ac516ab3d0f7121b3914365e82e
htslib/.git/objects/ec/
htslib/.git/objects/ec/c32eb4cf8d13e9c2705200e67402763d1a4b4d
htslib/.git/objects/29/
htslib/.git/objects/29/d9613036d807c86c4fa95b45190c5edd083cab
htslib/.git/objects/2e/
htslib/.git/objects/2e/9e19050ec2bc6a1904705a7d8cca52a9320b39
htslib/.git/objects/4b/
htslib/.git/objects/4b/646a70bf88bc0995b5be8f7a8e8511f53cfbf7
htslib/.git/objects/4b/2ad4f539779b519d20c6a9cdb5b9e786544a8b
htslib/.git/objects/8a/
htslib/.git/objects/8a/1d073707280c815607e35293bb9079616c7272
htslib/.git/objects/4c/
htslib/.git/objects/4c/82a74420393b253b34f6a8dfd28d190a1b7579
htslib/.git/objects/7d/
htslib/.git/objects/7d/beffcdcac3279b308ca26a9daa2af1a87f9a91
htslib/htslib.mk
htslib/kfunc.c
htslib/.travis.yml
htslib/regidx.c
htslib/vcf.5
htslib/md5.c
htslib/NEWS
htslib/vcf_sweep.c
htslib/vcfutils.c
htslib/config.h
htslib/htsfile.c
htslib/faidx.5
htslib/.gitattributes
make[2]: git: Command not found
make[2]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins/htslib'
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
In file included from bgzf.c:39:0:
htslib/bgzf.h:34:18: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
                  ^
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins/htslib'
make[1]: *** [htslib_target] Error 2
make[1]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins'
make: *** [trinity_essentials] Error 2

Thank you

[venu]

git: Command not found, install git and try again and also check this error with trinity installation

[iamtuttu5]

Dear h.mon thank you so much for you prompt reply

I am using ubuntu 14.04 , I tried the command as you suggested

sudo apt-get install zlib1g-devel command

it ouputs the following result

tuttu@kau:~$ sudo apt-get install zlib1g-devel
[sudo] password for tuttu:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package zlib1g-devel

[h.mon]

Wrong package name, sorry, try zlib1g-dev. And do not use the space reserved for answers, use comments instead to provide further information, to keep the forum tidy.

Answer 1

[h.mon]

Which Linux? You need the zlib development package, which provides zlib.h. On Ubuntu, if memory servers my right:

sudo apt-get install zlib1g-dev

edit: corrected package name, it was zlib1g-devel