Hi there
My newly installed Galaxy 18.01 server seems to be unable to install bowtie (the devteam version). I'm documenting my installation progress at:
http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/
As noted in the last paragraph:
"My next test was to try and install the bowtie2 tool from the toolshed. This failed, with the tool status going from New to Error with not much interesting left in the logs."
The log during the time when I'm trying to install bowtie2 is:
1. [pid: 8856|app: 0|req: 35/48] 10.8.0.2 () {48 vars in 1108 bytes} [Sun Mar 18 19:14:55 2018] GET /admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install => generated 650 bytes in 26 msecs (HTTP/1.1 302) 3headers in 269 bytes (1 switches on core 1) 2. 10.8.0.2 - - [18/Mar/2018:19:14:57 +0000] "GET /admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install HTTP/1.1" 302 - " https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6e..." "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36" 3. [pid: 8856|app: 0|req: 37/49] 10.8.0.2 () {48 vars in 1108 bytes} [Sun Mar 18 19:14:57 2018] GET /admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install => generated 650 bytes in 24 msecs (HTTP/1.1 302) 3headers in 269 bytes (1 switches on core 0) 4. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,375 [p:8856,w:2,m:0] [ uWSGIWorker2Core2] Dependency bowtie2 not found. 5. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,376 [p:8856,w:2,m:0] [ uWSGIWorker2Core2] Dependency samtools not found. 6. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [ uWSGIWorker2Core3] Dependency bowtie2 not found. 7. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [ uWSGIWorker2Core3] Dependency samtools not found. 8. 10.8.0.2 - - [18/Mar/2018:19:14:55 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6e..." "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36" 9. [pid: 8856|app: 0|req: 38/50] 10.8.0.2 () {48 vars in 1274 bytes} [Sun Mar 18 19:14:55 2018] GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 7001 msecs (HTTP/ 1.1 200) 2 headers in 73 bytes (1 switches on core 2) 10. 10.8.0.2 - - [18/Mar/2018:19:14:57 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6e..." "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36" 11. [pid: 8856|app: 0|req: 38/51] 10.8.0.2 () {48 vars in 1274 bytes} [Sun Mar 18 19:14:57 2018] GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 5987 msecs (HTTP/ 1.1 200) 2 headers in 73 bytes (1 switches on core 3) 12. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:14,128 [p:8846,w:1 ,m:0] [uWSGIWorker1Core1] Appending to tool panel section: Get Data 13. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:14,143 [p:8846,w:1 ,m:0] [uWSGIWorker1Core1] Appending to tool panel section: Get Data 14. 10.8.0.2 - - [18/Mar/2018:19:15:11 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install?changeset_revi..." "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146Safari/537.36" 15. [pid: 8846|app: 0|req: 14/52] 10.8.0.2 () {56 vars in 1329 bytes} [Sun Mar 18 19:15:11 2018] POST /admin_toolshed/prepare_for_install => generated 11133 bytes in 2509 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 1) 16. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:15,296 [p:8856,w:2 ,m:0] [uWSGIWorker2Core1] Appending to tool panel section: Get Data 17. 10.8.0.2 - - [18/Mar/2018:19:15:15 +0000] "POST /admin_toolshed/install_repositories HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64) AppleWebKit/537.36(KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 18. [pid: 8856|app: 0|req: 39/53] 10.8.0.2 () {54 vars in 1152 bytes} [Sun Mar 18 19:15:15 2018] POST /admin_toolshed/install_repositories => generated 20 bytes in 206 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 1) 19. 10.8.0.2 - - [18/Mar/2018:19:15:18 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 20. [pid: 8856|app: 0|req: 40/54] 10.8.0.2 () {54 vars in 1208 bytes} [Sun Mar 18 19:15:18 2018] POST /admin_toolshed/repository_installation_status_updates => generated 174 bytes in 17 msecs (HTTP/1.1 200) 4 headers in 110bytes (1 switches on core 2) 21. 10.8.0.2 - - [18/Mar/2018:19:15:21 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 22. [pid: 8856|app: 0|req: 41/55] 10.8.0.2 () {54 vars in 1208 bytes} [Sun Mar 18 19:15:21 2018] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 14 msecs (HTTP/1.1 200) 4 headers in 110 bytes (1 switches on core 3) 23. 10.8.0.2 - - [18/Mar/2018:19:15:24 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 24. [pid: 8846|app: 0|req: 15/56] 10.8.0.2 () {54 vars in 1208 bytes} [Sun Mar 18 19:15:24 2018] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 27 msecs (HTTP/1.1 200) 4 headers in 110 bytes (1 switches on core 3)
which doesn't seem terribly informative.
Any ideas? Thanks! Peter