add support for singularity

[zhan4429]

In the future updates, can you add support for singularity?

[atice]

Hi Yucheng, Sorry for the confusion. Could you please elaborate on you request so we could consider how best to support your request in future updates? Thank you for your interest in PhyloFisher! Alex Alexander K. Tice, Ph.D. Department of Biological Sciences Mississippi State University 027 Harned Hall Lab Telephone: 662-325-4008

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________________________________ From: Yucheng Zhang ***@***.***> Sent: Thursday, April 27, 2023 6:53 PM To: TheBrownLab/PhyloFisher ***@***.***> Cc: Subscribed ***@***.***> Subject: [TheBrownLab/PhyloFisher] add support for singularity (Issue #77) In the future updates, can you add support for singularity? — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/12llLoDmU40vxZwxI9j1OsTKG16TSD0Yv5j9KcYUAk-n8BhUxTptamM2I27rFkI-mKARbMgN6m5BS3UEjgozgqjWY-1VNK0STlifDxbeAOxHfEdXvJTgxBVwbsvl8gWlI_6rOckMb0fcw9M9MyVyA9po-ttKgRX7cUE-gggl7CLCRHkFF_5deLA5IOSp36Jil3hSCZLepkPPlt1PuNBI1lRng5SkrUVNxoJF_HcYibYf1JIicGCzHS4vIsjmTevpiAAjmza76UpfQVqbuRSM8Bl7h9yzNzpxKXl0OO3clBw6bJ2s8ijbO5jM1cx-Ejgnf/https%3A%2F%2Fgithub.com%2FTheBrownLab%2FPhyloFisher%2Fissues%2F77>, or unsubscribe<https://secure-web.cisco.com/1Zvd0Llqm9fxh5jqtTtrlCdTVxSCsXanT2wl33Ne3FYaxG062lRCXPLDv9yH4OJBsK3zok8UZRphxZt0vJatnBZ_1q84GqyUm7T6If-IzaKI5Aa_b_G64TX09IH6i6bUZRYd3GHoE0aZg6o5R62k3sjVnipcyPDdnDOLN2HNRTdsUnDfaT2cjvOjyXO0696f8_PuetNM1CIYIRtEuUUjNLQKhH-g2RzqcfzBqXzfxiHWbegzoIRrmZQyBf-0XBcRpCoCSObt6NeV6oRfnyxOiO2l_U3B3joEVrLPLvj4qC5brsyQs1dJ4Ez0j4XCDEB7D/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADA4OK3D53F57ANSOFTYEUTXDMBH7ANCNFSM6AAAAAAXOQV75Q>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[zhan4429]

Hi Alex,

Thanks for the quick response. I mean in your smk files, you only support conda environment, like below:

conda:
    'prequal.yaml'

I am wondering whether you can support singularity, like this:

singularity:
   ''docker://XXXX"

Best,
Yucheng

[atice]

Hi Yucheng, Thank you for you're comments. Another PhyloFisher team member clarified. We will certainly consider this and get back to you. Again, thank you for considering PhyloFisher for your work. Alex Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: Yucheng Zhang ***@***.***> Sent: Thursday, April 27, 2023 9:18:00 PM To: TheBrownLab/PhyloFisher ***@***.***> Cc: Tice, Alex ***@***.***>; Comment ***@***.***> Subject: Re: [TheBrownLab/PhyloFisher] add support for singularity (Issue #77) Hi Alex, Thanks for the quick response. I mean in your smk files, you only support conda environment, like below: conda: 'prequal.yaml' I am wondering whether you can support singularity, like this: singularity: ''docker://XXXX" Best, Yucheng — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/1ntemh6t3abxwT7uZL1Q543btaA6C1ykMJbQRNggkyAu1ScBSTS377gp-1Kp7M7DsxUSpnd1u-ro5lbIVxlLf1lI8uWw8fAPEsuuQidhtYCuLX662c3oxX8ATD-SxAop0RajWbUfwIcPuvJJK607sn2Gv1aPYgG6Al1bw7YbvD1byvvLF5e2qNtmUmqf_E_N5y0L9o-zaBkZBejMwZPl2a8vOTMgupbCpGj-kvY2q2O5SksSqd6JFpP5KRrsmXnrzOu-VxEJ0gNjgEA70dO07s6ciOth2r8IxFIZaDLDfBwHIFidKCl8o9jLZ0CwyRXUl/https%3A%2F%2Fgithub.com%2FTheBrownLab%2FPhyloFisher%2Fissues%2F77%23issuecomment-1526884276>, or unsubscribe<https://secure-web.cisco.com/1pNqQoWfDTAn3YmITMnFZOLO6sn2tF9wK7K_D779OrtjTP9DupPrJ0KzSRfwM-RZQ3wbixwHO1SQie5x9WreUWUELJNiohhMk5gYlX1ml6eZGRTSJvI3j2_AZ4L4Ns_bsh4Z9auvW1RSYFMQxZFXPJGgSMvKTBjHxnqoJT_4DjSLNdI_ZRVSNAa_U6GR2sJi7G89JhRC2fsVGIXBAm2iuiZjIUbpgEmKoDyV1JiTmn0ieaTiVaFf9vJJ4h2r2bPOlvZHUPb9dKU6-fxKB9JgLlLj3zZt-CM4mgkNUyaK9uZ8XA8BTYwGtd68uN2L_2zxr/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADA4OKYO2XBFT56MN7O62YTXDMSFRANCNFSM6AAAAAAXOQV75Q>. You are receiving this because you commented.Message ID: ***@***.***>

[robert-ervin-jones]

Hi Yucheng,

A Docker container for PhyloFisher can be found at quay.io/biocontainers/phylofisher.

Let me know if you have any more questions.

Best,
Robert