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opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
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three folders are empty in the downloaded cobratoolbox #1971

Open XuejianXiong opened 2 years ago

XuejianXiong commented 2 years ago

Hi there,

I am trying to install cobratoolbox using the following command "git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox". However, three folders, binary, papers and tutorials, are empty. I think it is because these three folders are named with @... Could you please solve this problem? Thanks!

Best, Xuejian

rmtfleming commented 2 years ago

Hi, have you checked your system is configured correctly before starting? https://opencobra.github.io/cobratoolbox/stable/installation.html Regards, Ronan

On Wed, 30 Mar 2022 at 15:51, Xuejian Xiong @.***> wrote:

Hi there,

I am trying to install cobratoolbox using the following command "git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox". However, three folders, binary, papers and tutorials, are empty. I think it is because these three folders are named with @... Could you please solve this problem? Thanks!

Best, Xuejian

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1971, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOQYKPJM6FPNSQGXQ7LVCRL57ANCNFSM5SCALHDA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

XuejianXiong commented 2 years ago

I installed git (2.34.1.windows.1 / linux 1.8.3.1) and curl (7.79.1 (Windows) / linux 7.29.0). I tried on both windows and linux, but have the same problem. Now I'm manually downloading these three folders one by one. Thanks!

rmtfleming commented 2 years ago

What is the response to: $ git --version

$ curl --version

On Wed, 30 Mar 2022 at 16:15, Xuejian Xiong @.***> wrote:

I installed git and curl. I also tried on both windows and linux. All the same problem. Now I'm manually downloading these three folders one by one.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

XuejianXiong commented 2 years ago

for linux 1) git version 1.8.3.1 2) curl 7.29.0 (x86_64-redhat-linux-gnu) libcurl/7.29.0 NSS/3.53.1 zlib/1.2.7 libidn/1.28 libssh2/1.8.0 Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtsp scp sftp smtp smtps telnet tftp Features: AsynchDNS GSS-Negotiate IDN IPv6 Largefile NTLM NTLM_WB SSL libz unix-sockets

for window: 1) git version 2.34.1.windows.1 2) curl 7.80.0 (x86_64-w64-mingw32) libcurl/7.80.0 OpenSSL/1.1.1l (Schannel) zlib/1.2.11 brotli/1.0.9 zstd/1.5.0 libidn2/2.3.1 libssh2/1.10.0 nghttp2/1.45.1 Release-Date: 2021-11-10 Protocols: dict file ftp ftps gopher gophers http https imap imaps ldap ldaps mqtt pop3 pop3s rtsp scp sftp smb smbs smtp smtps telnet tftp Features: alt-svc AsynchDNS brotli HSTS HTTP2 HTTPS-proxy IDN IPv6 Kerberos Largefile libz MultiSSL NTLM SPNEGO SSL SSPI TLS-SRP zstd

Thanks!

rmtfleming commented 2 years ago

Did you:

1.

Change to the folder cobratoolbox/ and run from [image: matlab]

initCobraToolbox

On Thu, 31 Mar 2022 at 14:55, Xuejian Xiong @.***> wrote:

for linux

  1. git version 1.8.3.1
  2. curl 7.29.0 (x86_64-redhat-linux-gnu) libcurl/7.29.0 NSS/3.53.1 zlib/1.2.7 libidn/1.28 libssh2/1.8.0 Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtsp scp sftp smtp smtps telnet tftp Features: AsynchDNS GSS-Negotiate IDN IPv6 Largefile NTLM NTLM_WB SSL libz unix-sockets

for window:

  1. git version 2.34.1.windows.1
  2. curl 7.80.0 (x86_64-w64-mingw32) libcurl/7.80.0 OpenSSL/1.1.1l (Schannel) zlib/1.2.11 brotli/1.0.9 zstd/1.5.0 libidn2/2.3.1 libssh2/1.10.0 nghttp2/1.45.1 Release-Date: 2021-11-10 Protocols: dict file ftp ftps gopher gophers http https imap imaps ldap ldaps mqtt pop3 pop3s rtsp scp sftp smb smbs smtp smtps telnet tftp Features: alt-svc AsynchDNS brotli HSTS HTTP2 HTTPS-proxy IDN IPv6 Kerberos Largefile libz MultiSSL NTLM SPNEGO SSL SSPI TLS-SRP zstd

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1971#issuecomment-1084622738, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQMEOU5KHT3WXYTPQZP5O3VCWVGDANCNFSM5SCALHDA . You are receiving this because you commented.Message ID: @.***>

--

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)