Library not loaded: @rpath/libtbbmalloc_proxy.dylib

[Rfriedmancolumbia]

./salmon index -t Mus_musculus.GRCm38.cdna.all.norm.fasta -i GRCm38.cdna.all_index --type quasi -l 31

Dear Salmon list,

I am using the Salmon 0.8.1 binary for Mac OS X, Sierra, 10.12.8. I am trying to set up an mm10 mouse index. I downlaod the mouse cDNAs from Ensembl, and normlized the ends with galaxy. I am running evelything in lib in case there are path issues. Here is my directory:

c2b2afmd2:lib friedman$ ls Mus_musculus.GRCm38.cdna.all.fa libtbbmalloc_proxy.dylib libtbb.dylib salmon libtbbmalloc.dylib

Here is my attemot to build an index:

c2b2afmd2:lib friedman$ ./salmon index -t Mus_musculus.GRCm38.cdna.all.norm.fasta -i GRCm38.cdna.all_index --type quasi -l 31 dyld: Library not loaded: @rpath/libtbbmalloc_proxy.dylib Referenced from: /Applications/Salmon-0.8.2_macOX_10.12/lib/./salmon Reason: image not found Abort trap: 6

I would greatly appreciate any help that you might be able ot give.

Thanks and best wishes, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Room 825 Irving Cancer Research Center
Columbia University Herbert and Florence Irving Medical Center 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) raf4@cumc.columbia.edu

http://www.columbia.edu/~raf4/index.html

“Will there still be "Classics Illustrated” by the time I have children? I cannot imagine raising kids without "Classics Illustrated” .” -Rose Friedman, age 20

[rob-p]

Hi Rich,

The issue with pre-compiled OSX binaries is that they are difficult to make portable across OSX versions. This is why we strongly suggest installing Salmon (especially for OSX) through Bioconda. This greatly eases installation and updating, and doesn't require admin privileges. On OSX, you can try the following:

$ conda config --add channels conda-forge
$ conda config --add channels bioconda
$ conda create -n salmon salmon=0.9.1

This should take care of all relevant dependencies as well as e.g. library locations and placement. Could you please give this a try and let me know if it works for you?

Best, Rob

[Rfriedmancolumbia]

Rob, Rob,

Thank you. It worked. I was able to make my index without error messages.

Best wishes, Rich

[Rfriedmancolumbia]

Rob,

I let you know on the forum page, but just ot make sure it worked and I was 

able to index my transcriptome.

Thank you!

Best wishes, Rich

On Apr 17, 2018, at 9:44 AM, Rob Patro notifications@github.com wrote:

Hi Rich,

The issue with pre-compiled OSX binaries is that they are difficult to make portable across OSX versions. This is why we strongly suggest installing Salmon (especially for OSX) through Bioconda. This greatly eases installation and updating, and doesn't require admin privileges. On OSX, you can try the following:

$ conda config --add channels conda-forge $ conda config --add channels bioconda $ conda create -n salmon salmon=0.9.1

This should take care of all relevant dependencies as well as e.g. library locations and placement. Could you please give this a try and let me know if it works for you?

Best, Rob

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Room 825 Irving Cancer Research Center
Columbia University Herbert and Florence Irving Medical Center 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) raf4@cumc.columbia.edu

http://www.columbia.edu/~raf4/index.html

“Will there still be "Classics Illustrated” by the time I have children? I cannot imagine raising kids without "Classics Illustrated” .” -Rose Friedman, age 20

[rob-p]

Great; glad to hear it worked!

Best, Rob