It seems to make 0 progress and is stuck at the modal "Install application. Please wait while the application is configured." Then an error pops up after a long time saying "zip headers not found. probably not a zip file" (same as in docker logs).
docker logs --timestamps adefde2f84c3 shows the full stacktrace
2019-12-24T01:05:35.617644000Z at java.lang.Thread.run(Thread.java:748)
2019-12-24T01:05:35.617687100Z Caused by: net.lingala.zip4j.exception.ZipException: zip headers not found. probably not a zip file
2019-12-24T01:05:35.617709500Z at net.lingala.zip4j.core.HeaderReader.readEndOfCentralDirectoryRecord(HeaderReader.java:122)
2019-12-24T01:05:35.617733600Z at net.lingala.zip4j.core.HeaderReader.readAllHeaders(HeaderReader.java:78)
2019-12-24T01:05:35.617757100Z at net.lingala.zip4j.core.ZipFile.readZipInfo(ZipFile.java:425)
2019-12-24T01:05:35.617780500Z at net.lingala.zip4j.core.ZipFile.extractAll(ZipFile.java:475)
2019-12-24T01:05:35.617852500Z at net.lingala.zip4j.core.ZipFile.extractAll(ZipFile.java:451)
2019-12-24T01:05:35.617893200Z at cloudgene.mapred.apps.ApplicationRepository.installFromZipFile(ApplicationRepository.java:350)
2019-12-24T01:05:35.617920200Z ... 55 more
2019-12-24T01:05:35.620071400Z 19/12/24 01:05:35 INFO LogService: 2019-12-24 01:05:35 172.17.0.1 - 172.17.0.2 80 POST /api/v2/server/apps - 400 115 100 110765 http://localhost:8080 Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/79.0.3945.79 Safari/537.36 http://localhost:8080/admin.html
2019-12-24T01:07:32.823620800Z /opt/cloudgene/cloudgene: line 24: 1567 Killed java -cp $CLASS_PATH $CLASS "$@"
I also tried installing an older version of the imputation server (v1.2.1). Installing cloudgene apps from the admin panel -- both via link and via apps.cloudgene.io -- doesn't work. Trying to update the imputation server from the admin panel ("Update to 1.2.4") also hangs with the same problem (see the comment of the same gist above https://gist.github.com/liezl200/4fecf9e375c15e26555ebbb42b4dda46).
(base) liezls-mbp:cloudgene lie$ ./cloudgene install https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip
Cloudgene 2.0.5
http://www.cloudgene.io
(c) 2009-2019 Lukas Forer and Sebastian Schoenherr
Built by travis on 2019-12-12T16:43:01Z
Built by travis on 2019-12-12T16:43:01Z
Installing application https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip...
It seems to make 0 progress and is stuck at the modal "Install application. Please wait while the application is configured." Then an error pops up after a long time saying "zip headers not found. probably not a zip file" (same as in docker logs).
docker logs --timestamps adefde2f84c3shows the full stacktracefull logs: https://gist.github.com/liezl200/4fecf9e375c15e26555ebbb42b4dda46
excerpt which looks relevant:
I tried all the installation methods from http://apps.cloudgene.io/imputationserver.1000genomes-phase3
I also tried installing an older version of the imputation server (v1.2.1). Installing cloudgene apps from the admin panel -- both via link and via apps.cloudgene.io -- doesn't work. Trying to update the imputation server from the admin panel ("Update to 1.2.4") also hangs with the same problem (see the comment of the same gist above https://gist.github.com/liezl200/4fecf9e375c15e26555ebbb42b4dda46).
Using cloudgene from command line just hangs:
full logs: https://gist.github.com/liezl200/bb8a4ee2c48af2cb788224aa3952e9cf