deepakunni3
commented
7 years ago Hi Luke,
Thanks for reporting this issue. Yes, we realized that there are issues with building Apollo. If you have a solution for this issue then feel free to create a PR.
We can take a look, make suggestions (if any) and then merge it.
Cheers,
Deepak
On Wed, Sep 13, 2017 at 4:15 PM, luke notifications@github.com wrote:
I am attempting to './apollo deploy' with a particular JBrowse plugin https://github.com/Yating-L/JBrowse_plugins, but get this error:
94 error code EISDIR 95 error errno -21 96 error syscall read 97 error eisdir EISDIR: illegal operation on a directory, read
Having given it the ol' Google/StackOverflow treatment, I suspect the change from bower dependency resolution has brought this on; I had no issues compiling a WAR file with the plugin in 2.0.6, but npm requires a 'package.json' in the repository for 'install' to work https://docs.npmjs.com/cli/install#description -- which this repo lacks.
Also, the previous version did not seem to need SSH configuration to be able to clone repos, presumably using https; this seems to be a consequence of the syntax chosen, as
git clone https://github.com/Yating-L/JBrowse_plugins.git
works without SSH configuration and
git clone git@github.com:Yating-L/JBrowse_plugins.git
does not.
It seems as though there are a few options:
- add an (empty?) package.json to the repo so that npm passes its superficial check
- revise the github installation logic to avoid using npm for plugins
- use the 'url' parameter to pass in files directly
speaking to the 'url' parameter options, i made some minor alterations to the source to test that out (right now it just tests to see if the URL parameter is true then copies whatever was linked to a file named after the plugin name https://github.com/GMOD/Apollo/blob/eb4764788909907013d02664742b6a99489480a7/build.gradle#L204), allowing you to set a 'zip' flag like in other areas of the build script. The issue there is that github archives contain the repo contents in a folder named after the repo, whereas other zip files linked to in the 'url' field have no such guarantee, so we are left unsure as to wether or not to move files from the base directory in the archive. One option is to check if the link supplied was a github link; these archives would always have their first level directory stripped, whereas default behavior would to leave the archive structure as is.
So, in summary: JBrowse plugin installation is giving me guff; I can see a few ways to resolve the issue and am happy to make whatever changes and issue a pull request, but wanted to see what the prevailing opinion was.
If there's any more information I can provide, do let me know.
Thanks, -Luke
relevant apollo-config.groovy snippet:
plugins { "G-OnRamp_plugin"{ git= "https://github.com/Yating-L/JBrowse_plugins" branch = "master" }— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/1752, or mute the thread https://github.com/notifications/unsubscribe-auth/AEUgYAlEBoOc0Pm9j9qf2WP_GmRQQqMTks5siEX2gaJpZM4PWvO6 .
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nathandunn
luke-c-sargent
I am attempting to './apollo deploy' with a particular JBrowse plugin, but get this error:
Having given it the ol' Google/StackOverflow treatment, I suspect the change from bower dependency resolution has brought this on; I had no issues compiling a WAR file with the plugin in 2.0.6, but npm requires a 'package.json' in the repository for 'install' to work -- which this repo lacks.
Also, the previous version did not seem to need SSH configuration to be able to clone repos, presumably using https; this seems to be a consequence of the syntax chosen, as
works without SSH configuration and
does not.
It seems as though there are a few options:
speaking to the 'url' parameter options, i made some minor alterations to the source to test that out (right now it just tests to see if the URL parameter is true then copies whatever was linked to a file named after the plugin name), allowing you to set a 'zip' flag like in other areas of the build script. The issue there is that github archives contain the repo contents in a folder named after the repo, whereas other zip files linked to in the 'url' field have no such guarantee, so we are left unsure as to wether or not to move files from the base directory in the archive. One option is to check if the link supplied was a github link; these archives would always have their first level directory stripped, whereas default behavior would to leave the archive structure as is.
So, in summary: JBrowse plugin installation is giving me guff; I can see a few ways to resolve the issue and am happy to make whatever changes and issue a pull request, but wanted to see what the prevailing opinion was.
If there's any more information I can provide, do let me know.
Thanks, -Luke
relevant apollo-config.groovy snippet: