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vsbuffalo / zmays_germinate

Download and create local Zea mays resouces
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make? #1

Open rossibarra opened 10 years ago

rossibarra commented 10 years ago

I clone repo, run "make" and nothing happens except a few directories are created?

vsbuffalo commented 10 years ago

Try make all. Note that you can set the AGP version in the Makefile.

rossibarra commented 10 years ago

Downloads fine, but error (presumably because on Farm at least gzcat doesn’t exist but zcat does).

INISHED --2014-02-28 14:59:34-- Total wall clock time: 8m 51s Downloaded: 12 files, 590M in 8m 11s (1.20 MB/s) touch data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.1.fa.gz (gzcat data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.1.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.2.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.3.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.4.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.5.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.6.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.7.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.8.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.9.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.10.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.mitochondrion.fa.gz data/AGPv2.17/seqs/Zea_mays.AGPv2.17.dna.chromosome.chloroplast.fa.gz > data/AGPv2.17/seqs/AGPv2.17_combined.fa) /bin/sh: gzcat: command not found make: *\ [data/AGPv2.17/seqs/AGPv2.17_combined.fa] Error 127

On Feb 28, 2014, at 11:01 AM, Vince Buffalo notifications@github.com wrote:

Try make all. Note that you can set the AGP version in the Makefile.

— Reply to this email directly or view it on GitHub.

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Web: www.rilab.org Twitter: @jrossibarra Tel: 530-752-1152 Fax: 530-752-4604

vsbuffalo commented 10 years ago

Yea, had this issue. Forgot to document this, but just adjust this:

https://github.com/vsbuffalo/zmays_germinate/blob/master/Makefile#L9

rossibarra commented 10 years ago

Yup already did and rerunning.

-J

On Feb 28, 2014, at 3:08 PM, Vince Buffalo notifications@github.com wrote:

Yea, had this issue. Forgot to document this, but just adjust this:

https://github.com/vsbuffalo/zmays_germinate/blob/master/Makefile#L9

— Reply to this email directly or view it on GitHub.

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Web: www.rilab.org Twitter: @jrossibarra Tel: 530-752-1152 Fax: 530-752-4604