pipefail fails in zsh

[mojaveazure]

pipefail fails in zsh

[mojaveazure]

[mojaveazure]

Wright MH, et al. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 2010;26(23):2952-60

[rossibarra]

Sorry I miss the reference. Do they say something about pipe fail and zsh?

---

Jeffrey Ross-Ibarra

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

Tel: [phone]
@jrossibarra
www.rilab.org

On Fri, Feb 5, 2016 at 2:17 PM, Paul Hoffman [email protected]
wrote:

Wright MH, et al. ALCHEMY: a reliable method for automated SNP genotype
calling for small batch sizes and highly homozygous populations.
Bioinformatics 2010;26(23):2952-60

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#33 (comment)
.

[mojaveazure]

When @liux1299 runs AW in zsh, it works for her. The issue referenced says that zsh versions 5.0.7 has set -o pipefail; which version of zsh are you running?

[rossibarra]

Yeah saw and checked that:

[ 2:22PM ] [ jri@Jeffreys-MacBook-Pro-2:~/Projects/wang_paper/demography/manuscript(master✗)
]
$ zsh --version
zsh 5.0.8 (x86_64-apple-darwin15.0)

---

Jeffrey Ross-Ibarra

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

Tel: [phone]
@jrossibarra
www.rilab.org

On Fri, Feb 5, 2016 at 2:39 PM, Paul Hoffman [email protected]
wrote:

When @liux1299 https://github.com/liux1299 runs AW in zsh, it works for
her. The issue referenced says that zsh versions 5.0.7 has set -o pipefail;
which version of zsh are you running?

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#33 (comment)
.

[ChaochihL]

Was able to run with my version:

[liux1299@labqi046]~/ANGSD-wrapper_beta_testing/angsd-wrapper/Example_Data/Maize/Configuration_Files% echo $ZSH_VERSION
4.3.11

[rossibarra]

Intersting, will test again.

---

Jeffrey Ross-Ibarra

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

Tel: [phone]
@jrossibarra
www.rilab.org

On Fri, Feb 5, 2016 at 2:46 PM, ChaochihLiu [email protected]
wrote:

Was able to run with my version:

[liux1299@labqi046]~/ANGSD-wrapper_beta_testing/angsd-wrapper/Example_Data/Maize/Configuration_Files% echo $ZSH_VERSION
4.3.11

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#33 (comment)
.

[mojaveazure]

I can run as well

paul@Freya-x220:~/angsd-wrapper/Example_Data/Sequences$ zsh --version
zsh 5.1.1 (x86_64-ubuntu-linux-gnu)