Closed mictadlo closed 8 years ago
bgruening
commented
8 years ago @mvdbeek https://github.com/galaxyproject/ansible-galaxy-extras/pull/43 This should also fix your latest problem @mictadlo.
Regarding your first issue, I found this: https://github.com/docker/docker/issues/15538 Does this help you in any way?
mictadlo
commented
8 years ago Thank you, on the VM without BTRFS partition ipython, jupyter and rstudio are loading. However, I get now "Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:27:25.058260050Z" level=error msg="Handler for POST /v1.21/containers/create returned error: No such image: bgruening/docker-ipython-notebook:15.10.1"
time="2016-01-13T03:27:25.058290669Z" level=error msg="HTTP Error" err="No such image: bgruening/docker-ipython-notebook:15.10.1" statusCode=404
time="2016-01-13T03:27:25.058807223Z" level=info msg="POST /v1.21/images/create?fromImage=bgruening%2Fdocker-ipython-notebook&tag=15.10.1"
time="2016-01-13T03:27:58.190475742Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:28:23.033877563Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:29:40.575185450Z" level=info msg="POST /v1.21/containers/create"
time="2016-01-13T03:29:40.616726082Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:29:40.628506277Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:29:40.640672494Z" level=info msg="POST /v1.21/containers/35be27c6fe02820d709c8bfeab56750672c76f663f7bd7242d56b97f0e129616/start"
time="2016-01-13T03:30:41.487441382Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:34:19.505308428Z" level=info msg="POST /v1.21/containers/create"
time="2016-01-13T03:34:19.518320416Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:34:19.533350661Z" level=error msg="Couldn't run auplink before unmount: exec: \"auplink\": executable file not found in $PATH"
time="2016-01-13T03:34:19.545178610Z" level=info msg="POST /v1.21/containers/40965c555abc87643a0cd68ded9fd6536b2a496b50ca1521a75c265312c0b903/start"
time="2016-01-13T03:34:19.834095658Z" level=info msg="GET /v1.21/containers/40965c555abc87643a0cd68ded9fd6536b2a496b50ca1521a75c265312c0b903/json"My second problem is when I tried to use IPython with the following code:
with open( get( 1 ), 'r') as handle:
for line in handle:
print( line )Than I received the following problems:
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
<ipython-input-3-7842fca36ab2> in <module>()
----> 1 with open( get( 1 ), 'r') as handle:
2 for line in handle:
3 print( line )
/home/ipython/py/galaxy.pyc in get(dataset_id, history_id)
120 # The object version of bioblend is to slow in retrieving all datasets from a history
121 # fallback to the non-object path
--> 122 gi = get_galaxy_connection(history_id=history_id, obj=False)
123
124 file_path = '/import/%s' % dataset_id
/home/ipython/py/galaxy.pyc in get_galaxy_connection(history_id, obj)
96 ### Fail ###
97 msg = "Could not connect to a galaxy instance. Please contact your SysAdmin for help with this error"
---> 98 raise Exception(msg)
99
100
Exception: Could not connect to a galaxy instance. Please contact your SysAdmin for help with this errorWhat did I do wrong?
dpryan79
commented
8 years ago I'm getting a similar error on a fresh pull:
Exception Traceback (most recent call last)
<ipython-input-1-583038ebeffd> in <module>()
----> 1 fh = open(get(1), "r")
2 chroms = []
3 for line in fh:
4 l1 = line.strip().split()
5 if l1[0] not in chroms:
/home/jovyan/py/galaxy.py in get(dataset_id, history_id)
115 history_id = history_id or os.environ['HISTORY_ID']
116
--> 117 gi = get_galaxy_connection(history_id=history_id)
118
119 file_path = '/import/%s' % dataset_id
/home/jovyan/py/galaxy.py in get_galaxy_connection(history_id)
92 ### Fail ###
93 msg = "Could not connect to a galaxy instance on %s. Please contact your SysAdmin for help with this error" % url
---> 94 raise Exception(msg)
95
96
Exception: Could not connect to a galaxy instance on http://172.18.0.1:None. Please contact your SysAdmin for help with this errorI wonder if there's a port that needs to get filled in somewhere.
N.B., I'm using quay.io/bgruening/galaxy:dev
bgruening
commented
8 years ago @dpryan79 can you try to access your Galaxy with a proper URI, so your hostname for example and not localhost? Also please try :16.01
dpryan79
commented
8 years ago @bgruening Apparently not, should be easy enough to solve. I'll also switch to 16.01
mictadlo
commented
8 years ago Thank you it works with http://10.0.2.15:8080/ and
docker run -d -p 8080:80 -p 8800:8800 -p 9002:9002 --privileged=true -v /home/galaxy/galaxy_storage/:/export -e "GALAXY_LOGGING=full" quay.io/bgruening/galaxy:16.01@bgruening Works now, silly routing issue.
bgruening
commented
8 years ago Awesome! Sorry for the trouble.
Hello, I am still no able to use IE (Rstudio and Ipython). The logs show the following:
127.0.0.1 - - [30/Dec/2015:01:55:06 +0000] "GET /visualization/show/rstudio?dataset_id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 189|app: 0|req: 10/15] 172.17.0.1 () {48 vars in 928 bytes} [Wed Dec 30 01:55:06 2015] GET /visualization/show/rstudio?dataset_id=f2db41e1fa331b3e => generated 1559 bytes in 1077 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 2) 127.0.0.1 - - [30/Dec/2015:01:55:07 +0000] "GET /plugins/interactive_environments/rstudio/static/js/crypto/prng4.js HTTP/1.1" 404 - "http://localhost/visualization/show/rstudio?dataset_id=f2db41e1fa331b3e" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" 127.0.0.1 - - [30/Dec/2015:01:55:07 +0000] "GET /plugins/interactive_environments/rstudio/static/js/crypto/rng.js HTTP/1.1" 404 - "http://localhost/visualization/show/rstudio?dataset_id=f2db41e1fa331b3e" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 189|app: 0|req: 12/16] 172.17.0.1 () {52 vars in 1041 bytes} [Wed Dec 30 01:55:07 2015] GET /plugins/interactive_environments/rstudio/static/js/crypto//rng.js => generated 304 bytes in 1 msecs (HTTP/1.1 404) 1 headers in 51 bytes (1 switches on core 1) [pid: 189|app: 0|req: 12/17] 172.17.0.1 () {52 vars in 1045 bytes} [Wed Dec 30 01:55:07 2015] GET /plugins/interactive_environments/rstudio/static/js/crypto//prng4.js => generated 306 bytes in 1 msecs (HTTP/1.1 404) 1 headers in 51 bytes (1 switches on core 3) 127.0.0.1 - - [30/Dec/2015:01:55:07 +0000] "GET /plugins/interactive_environments/rstudio/static/js/crypto/rsa.js HTTP/1.1" 404 - "http://localhost/visualization/show/rstudio?dataset_id=f2db41e1fa331b3e" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 189|app: 0|req: 13/18] 172.17.0.1 () {52 vars in 1041 bytes} [Wed Dec 30 01:55:07 2015] GET /plugins/interactive_environments/rstudio/static/js/crypto//rsa.js => generated 304 bytes in 0 msecs (HTTP/1.1 404) 1 headers in 51 bytes (1 switches on core 0) 127.0.0.1 - - [30/Dec/2015:01:55:07 +0000] "GET /plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js HTTP/1.1" 404 - "http://localhost/visualization/show/rstudio?dataset_id=f2db41e1fa331b3e" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 188|app: 0|req: 6/19] 172.17.0.1 () {52 vars in 1044 bytes} [Wed Dec 30 01:55:07 2015] GET /plugins/interactive_environments/rstudio/static/js/crypto//jsbn.js => generated 305 bytes in 0 msecs (HTTP/1.1 404) 1 headers in 51 bytes (1 switches on core 1) 127.0.0.1 - - [30/Dec/2015:01:55:07 +0000] "GET /plugins/interactive_environments/rstudio/static/js/crypto/base64.js HTTP/1.1" 404 - "http://localhost/visualization/show/rstudio?dataset_id=f2db41e1fa331b3e" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 189|app: 0|req: 14/20] 172.17.0.1 () {52 vars in 1047 bytes} [Wed Dec 30 01:55:07 2015] GET /plugins/interactive_environments/rstudio/static/js/crypto//base64.js => generated 307 bytes in 0 msecs (HTTP/1.1 404) 1 headers in 51 bytes (1 switches on core 2) 127.0.0.1 - - [30/Dec/2015:01:55:07 +0000] "GET /plugins/interactive_environments/rstudio/static/js/rstudio.js HTTP/1.1" 404 - "http://localhost/visualization/show/rstudio?dataset_id=f2db41e1fa331b3e" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 189|app: 0|req: 15/21] 172.17.0.1 () {52 vars in 1035 bytes} [Wed Dec 30 01:55:07 2015] GET /plugins/interactive_environments/rstudio/static/js//rstudio.js => generated 301 bytes in 0 msecs (HTTP/1.1 404) 1 headers in 51 bytes (1 switches on core 1) galaxy.web.base.interactive_environments INFO 2015-12-30 01:56:03,145 Starting docker container for IE ipython with command [docker run --sig-proxy=true -e DEBUG=false -e "GALAXY_URL=http:/" -e "CORS_ORIGIN=http://localhost" -e "HISTORY_ID=f597429621d6eb2b" -e "NOTEBOOK_PASSWORD=none" -e "DATASET_HID=None" -e "PROXY_PREFIX=" -e "API_KEY=190fc21dcc3277504939d12b8767b8b8" -e "REMOTE_HOST=127.0.0.1" -e "USER_EMAIL=m.lorenc@qut.edu.au" -d -P bgruening/docker-ipython-notebook:15.10.1] galaxy.web.base.interactive_environments DEBUG 2015-12-30 01:56:03,648 Container id: fd11f6b411a2c81e5b343bee42d6ae26298d3b4507b23e5397bd1ecd2f6deb6b
galaxy.web.base.interactive_environments INFO 2015-12-30 01:56:03,648 Inspecting docker container fd11f6b411a2c81e5b343bee42d6ae26298d3b4507b23e5397bd1ecd2f6deb6b with command [docker inspect fd11f6b411a2c81e5b343bee42d6ae26298d3b4507b23e5397bd1ecd2f6deb6b ] 127.0.0.1 - - [30/Dec/2015:01:56:03 +0000] "GET /visualization/show/ipython?dataset_id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101 Firefox/43.0" [pid: 188|app: 0|req: 7/22] 172.17.0.1 () {48 vars in 928 bytes} [Wed Dec 30 01:56:03 2015] GET /visualization/show/ipython?dataset_id=f2db41e1fa331b3e => generated 1366 bytes in 661 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 3)
What did I do wrong?
Mic