Trinity on Mac OS

[Amel]

Hi, does trinity work on Mac OS please??

I tried to make a test but i have this result on the terminal:

MacBook-Pro-de-Amel:trinityrnaseq-2.2.0 pitch$ make test

Checking for Trinity essentials (built from 'make all'):

sh ./util/support_scripts/trinity_install_tests.sh

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Performing Unit Tests of Build

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

JellyFish                Installation appears to have FAILED

Inchworm Installation appears to have FAILED

Chrysalis Installation appears to have FAILED

QuantifyGraph Installation appears to have FAILED

GraphFromFasta Installation appears to have FAILED

ReadsToTranscripts Installation appears to have FAILED

fastool Installation appears to have FAILED

parafly Installation appears to have FAILED

samtools-0.1.19 Installation appears to have FAILED

Checking for plugins (built from 'make plugins'):

sh ./util/support_scripts/plugin_install_tests.sh

## Checking plugin installations:

slclust Installation appears to have FAILED

collectl Installation appears to have FAILED

Can you help me please??

Thanks a lot

[Brian Haas]

I regularly build it on mac and test it on small data sets.  It does require that you have a relatively new version of GCC installed (try homebrew for easiest installation).

Trinity is targeted towards Linux, though, and should run on a high-memory server (~1G RAM per ~1M PE reads as a very rough estimate).

~brian

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Amel]

Thank you Brian for the reply!!

Finally i decided to work on linux, ans now i have a little strange error, i don't know if i've to call this an "error" anyway :/

Trinity version: v2.1.1

-ERROR: couldn't run the network check to confirm latest Trinity software version.

Friday, June 3, 2016: 10:33:19 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/amelmek/anaconda2/opt/trinity-2.1.1/util/support_scripts/ExitTester.jar 0

Friday, June 3, 2016: 10:33:19 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/amelmek/anaconda2/opt/trinity-2.1.1/util/support_scripts/ExitTester.jar 1

----------------------------------------------------------------------------------

-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------

----------------------------------------------------------------------------------

#######################################################################

Inchworm file: /home/amelmek/trinity_out_dir/inchworm.K25.L25.DS.fa detected.

Skipping Inchworm Step, Using Previous Inchworm Assembly

#######################################################################

-- Skipping CMD: /home/amelmek/anaconda2/opt/trinity-2.1.1/util/misc/fasta_filter_by_min_length.pl /home/amelmek/trinity_out_dir/inchworm.K25.L25.DS.fa 100 > /home/amelmek/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100, checkpoint exists.

-- Skipping CMD: /home/amelmek/anaconda2/opt/trinity-2.1.1/Chrysalis/GraphFromFasta -i /home/amelmek/trinity_out_dir/inchworm.K25.L25.DS.fa -r both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 3 -k 24 -kk 48  > /home/amelmek/trinity_out_dir/chrysalis/GraphFromIwormFasta.out, checkpoint exists.

-- Skipping CMD: /home/amelmek/anaconda2/opt/trinity-2.1.1/Chrysalis/CreateIwormFastaBundle -i /home/amelmek/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /home/amelmek/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint exists.

-- Skipping CMD: /home/amelmek/anaconda2/opt/trinity-2.1.1/Chrysalis/ReadsToTranscripts -i both.fa -f /home/amelmek/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /home/amelmek/trinity_out_dir/chrysalis/readsToComponents.out -t 3 -max_mem_reads 50000000 , checkpoint exists.

-- Skipping CMD: /usr/bin/sort --parallel=3 -T . -S 2G -k 1,1n /home/amelmek/trinity_out_dir/chrysalis/readsToComponents.out > /home/amelmek/trinity_out_dir/chrysalis/readsToComponents.out.sort, checkpoint exists.

Friday, June 3, 2016: 10:33:19 CMD: /home/amelmek/anaconda2/opt/trinity-2.1.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file partitioned_reads.files.list --CPU 1 --max_memory 1G  --seqType fa --trinity_complete --full_cleanup  --min_kmer_cov  2  > recursive_trinity.cmds

####################################################################################

#

#  usage: /home/amelmek/anaconda2/opt/trinity-2.1.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file <string> [Trinity params]

#

# Required:

#

# --reads_list_file <string>      file containing list of filenames corresponding 

#                                  to the reads.fasta

#

#

#####################################################################################

Trinity run failed. Must investigate error above.

HELPPPPP !!! :(