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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Problem with executing Pilon #140

Open Hai1983 opened 3 years ago

Hai1983 commented 3 years ago

I succeed to download into my home directory. But when I executed it: “ ./build.sh”, it not succeed .!

“daomhai@nic5-login1 ~/software/pilon-1.24 $ ./build.sh fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). ./build.sh: line 14: sbt: command not found ln: failed to create symbolic link '/home/ulg/bbasv/daomhai/lib/pilon/pilon-dev.jar': No such file or directory”

Please give me some advise on executing this!!

Thanks you in advance for your help.

Sincerely, Hai

w1bw commented 3 years ago

The build.sh script is only for building from source, and assumes that it is in a checked out git repo.

All you should need to run pilon is the pilon.jar file for the release.

--bruce

On Mon, Nov 22, 2021 at 5:07 PM Hai1983 @.***> wrote:

I succeed to download into my home directory. But when I executed it: “ ./build.sh”, it not succeed .!

@.*** ~/software/pilon-1.24 $ ./build.sh fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). ./build.sh: line 14: sbt: command not found ln: failed to create symbolic link '/home/ulg/bbasv/daomhai/lib/pilon/pilon-dev.jar': No such file or directory”

Please give me some advise on executing this!!

Thanks you in advance for your help.

Sincerely, Hai

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/pilon/issues/140, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABLUSIY22WWR3VGIZ3ET33UNK5KBANCNFSM5ISCGJXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Hai1983 commented 3 years ago

Many thanks!

I got it,

Sincerely Hai

Sent from my iPhone

On 23 Nov 2021, at 15:24, Bruce Walker @.***> wrote:

The build.sh script is only for building from source, and assumes that it is in a checked out git repo.

All you should need to run pilon is the pilon.jar file for the release.

--bruce

On Mon, Nov 22, 2021 at 5:07 PM Hai1983 @.***> wrote:

I succeed to download into my home directory. But when I executed it: “ ./build.sh”, it not succeed .!

@.*** ~/software/pilon-1.24 $ ./build.sh fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). ./build.sh: line 14: sbt: command not found ln: failed to create symbolic link '/home/ulg/bbasv/daomhai/lib/pilon/pilon-dev.jar': No such file or directory”

Please give me some advise on executing this!!

Thanks you in advance for your help.

Sincerely, Hai

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/pilon/issues/140, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABLUSIY22WWR3VGIZ3ET33UNK5KBANCNFSM5ISCGJXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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