Re: [galaxy-dev] Problems installing Galaxy 18.01
Thanks to Marius and others, I now have a working Galaxy server, including
CVMFS support, as documented in the complete blog post:
http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/
The problem I was encountering with installations was related to incorrect
environment configuration, which led to the `hg` binary not being found in
the PATH and thus the install failing. Another fault led to this failure
being a silent failure.
I've linked to the working configuration in the blog, but here is a direct
link:
https://gist.github.com/pvanheus/589f84507a26ffa49e3bdf3bd938f25c
It is rather too unwieldy to paste here.
Note that while the says [program:web], there is only one section in the
supervisord configuration. The server is running in a uWSGI + Mules
configuration.
Thanks!
Peter
On Mon, 19 Mar 2018 at 11:17 Peter van Heusden wrote:
> First to answer your questions:
>
> I'm on release_18.01 branch,
> commit c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999.
>
> Thanks for the note about nginx-extras, I've installed that and it fixes
> the upload
> directives problem.
>
> Then on to the main problem. I used "Get Data" as the default location
> because I'm really just testing the install. The install goes from "New"
> status to "Error" status pretty much immediately:
>
> [image: image.png]
>
> This is not a bowtie2-specific problem, I get the same behaviour when
> trying to install fastqc.
>
> Thanks for your reply,
> Peter
> P.S. running already-installed tools works
>
> On Mon, 19 Mar 2018 at 09:44 Marius van den Beek
> wrote:
>
>> Hi Peter,
>>
>> does the tool show up in the tool panel (Looks like you've installed it
>> into "Get Data")?
>> What commit are you on ? There were some last minute bugfixes to the
>> release_18.01
>> prior to the release, so if the checkout is a few days old an upgrade
>> (and an uninstall/install cycle) might help.
>>
>> Also you mentioned the lack of the upload_store in nginx in nginx, you
>> need to install nginx-extras, not nginx.
>>
>> Hope that helps,
>> Marius
>>
>> On 18 March 2018 at 21:17, Peter van Heusden wrote:
>>
>>> 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 +] "GET
>>>/admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install
>>>HTTP/1.1" 302 - "
>>>
>>> https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6eb2b";
>>>"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 +] "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=f597429621d6eb2b";
>>>"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
Re: [galaxy-dev] Problems installing Galaxy 18.01
First to answer your questions:
I'm on release_18.01 branch,
commit c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999.
Thanks for the note about nginx-extras, I've installed that and it fixes
the upload
directives problem.
Then on to the main problem. I used "Get Data" as the default location
because I'm really just testing the install. The install goes from "New"
status to "Error" status pretty much immediately:
[image: image.png]
This is not a bowtie2-specific problem, I get the same behaviour when
trying to install fastqc.
Thanks for your reply,
Peter
P.S. running already-installed tools works
On Mon, 19 Mar 2018 at 09:44 Marius van den Beek
wrote:
> Hi Peter,
>
> does the tool show up in the tool panel (Looks like you've installed it
> into "Get Data")?
> What commit are you on ? There were some last minute bugfixes to the
> release_18.01
> prior to the release, so if the checkout is a few days old an upgrade (and
> an uninstall/install cycle) might help.
>
> Also you mentioned the lack of the upload_store in nginx in nginx, you
> need to install nginx-extras, not nginx.
>
> Hope that helps,
> Marius
>
> On 18 March 2018 at 21:17, Peter van Heusden wrote:
>
>> 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 +] "GET
>>/admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install
>>HTTP/1.1" 302 - "
>>
>> https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6eb2b";
>>"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 +] "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=f597429621d6eb2b";
>>"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 +] "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=f597429621d6eb2b";
>>"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] [uWS
Re: [galaxy-dev] Problems installing Galaxy 18.01
Hi Peter,
does the tool show up in the tool panel (Looks like you've installed it
into "Get Data")?
What commit are you on ? There were some last minute bugfixes to the
release_18.01
prior to the release, so if the checkout is a few days old an upgrade (and
an uninstall/install cycle) might help.
Also you mentioned the lack of the upload_store in nginx in nginx, you need
to install nginx-extras, not nginx.
Hope that helps,
Marius
On 18 March 2018 at 21:17, Peter van Heusden wrote:
> 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 +] "GET
>/admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install
>HTTP/1.1" 302 - "https://galaxy.sanbi.ac.za/admin_toolshed/manage_
>repository?id=f597429621d6eb2b" "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 +] "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=f597429621d6eb2b" "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 +] "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=f597429621d6eb2b" "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 +] "POST
>/admin_toolshed/prepare_for_install HTTP/1.1" 200 - "
>https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_
>install?changeset_revisions=dc1639b66f12&repository_ids=
>126c0918b5459666&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
>
>
