Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput
OK!!! Thanks it's more clear for me.
So I've a bug!
I've followed your instructions. the DeleteAction is attached to the final
step of my workflow. Before this, 2 steps exist with one output dataset not
marked as output of workflow for each of this 2 step.
The dataset of my first step is hidden and deleted : good!
But the dataset of my second step is hidden but not deleted ! I don't
understand why
Thanks
Julie
2014-09-23 15:49 GMT+02:00 Dannon Baker :
> Hi Julie,
>
> You don't attach the 'Delete Intermediate Datasets' action to a dataset
> you want to delete -- you attach it to one of the 'final' output steps of
> your workflow, at which point the action will clean up all datasets up to
> that point.
>
> So, for a simple example, see this workflow for selecting random FASTA
> lines from FASTQ.
>
> [image: Inline image 1]
>
>
> "Select random lines" is flagged as an output step, and the "Delete
> Intermediates" action is attached to it. When the workflow runs, the FASTQ
> to FASTA step will be deleted.
>
> More detail from the "Run workflow" page, showing the attached action:
>
> [image: Inline image 2]
>
>
> Does that help explain things?
>
> -Dannon
>
>
> On Tue, Sep 23, 2014 at 9:37 AM, julie dubois wrote:
>
>> Hi Dannon,
>>
>> Thanks for your answer. Sorry but I think I don't understand all of
>> your explanations.
>>
>> First : if an output is marked with a highlighted snowflake, it will
>> be not deleted : it's OK
>> Second : if a dataset is used in several steps of my workflow, it will
>> be deleted when all these steps will be terminated : it's OK
>>
>> But : "Perhaps the confusion is that they're also marked as 'hidden'
>> since they are not output steps?"
>> I don't understand :
>> so in my mind, when the dataset is marked with a grey snowflake, it is
>> automatically hidden and it's translated in the file of the workflow
>> with this code :
>> "post_job_actions": {
>> "HideDatasetActionout_file1": {
>> "action_arguments": {},
>> "action_type": "HideDatasetAction",
>> "output_name": "out_file1"
>> }
>> },
>>
>>
>> But when I add another postJobAction to such dataset , with this
>> translation in the workflow file :
>> "post_job_actions": {
>> "HideDatasetActionout_file1": {
>> "action_arguments": {},
>> "action_type": "HideDatasetAction",
>> "output_name": "out_file1"
>> },
>> "DeleteIntermediatesActionout_file1": {
>> "action_arguments": {},
>> "action_type": "DeleteIntermediatesAction",
>> "output_name": "out_file1"
>> }
>> },
>>
>> The result in my history is an hidden dataset (visible when I chek the
>> hisotry option "include hidden dataset") but not a deleted dataset
>> (visible when I chek the history option "include deleted datasets")
>> And it is the case for datasets used in several steps of workflow AND
>> for dataset which is just an output of a job not used in an other job.
>>
>> Is an hidden dataset not deletable ?
>> I've changed the order of postJobActions in the file, but no effect.
>> And If I remove the "HideDatasetAction", the dataset is not removed
>> because it become marked with highligthed snowflake.
>>
>> So is your final purpose the alone solution to delete intermediates
>> datasets ? And if I correctly understand, I must create a tool that
>> take all my deletable datasets as input and which will remove all of
>> these. In this case, the postJobAction "DeleteIntermediates" is not
>> usefull, is it ?
>>
>> Thanks.
>>
>> Julie
>>
>> 2014-09-23 14:15 GMT+02:00 Dannon Baker :
>> > Hi Julie!
>> >
>> > The action resolves at the completion time of the job it is attached to,
>> > deleting datasets of any other already-completed jobs in that workflow
>> which
>> > are not marked as an output step (with a highlighted snowflake). This
>> will
>> > *not* delete datasets of any job marked as an output.
>> >
>>
Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput
Hi Dannon,
Thanks for your answer. Sorry but I think I don't understand all of
your explanations.
First : if an output is marked with a highlighted snowflake, it will
be not deleted : it's OK
Second : if a dataset is used in several steps of my workflow, it will
be deleted when all these steps will be terminated : it's OK
But : "Perhaps the confusion is that they're also marked as 'hidden'
since they are not output steps?"
I don't understand :
so in my mind, when the dataset is marked with a grey snowflake, it is
automatically hidden and it's translated in the file of the workflow
with this code :
"post_job_actions": {
"HideDatasetActionout_file1": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "out_file1"
}
},
But when I add another postJobAction to such dataset , with this
translation in the workflow file :
"post_job_actions": {
"HideDatasetActionout_file1": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "out_file1"
},
"DeleteIntermediatesActionout_file1": {
"action_arguments": {},
"action_type": "DeleteIntermediatesAction",
"output_name": "out_file1"
}
},
The result in my history is an hidden dataset (visible when I chek the
hisotry option "include hidden dataset") but not a deleted dataset
(visible when I chek the history option "include deleted datasets")
And it is the case for datasets used in several steps of workflow AND
for dataset which is just an output of a job not used in an other job.
Is an hidden dataset not deletable ?
I've changed the order of postJobActions in the file, but no effect.
And If I remove the "HideDatasetAction", the dataset is not removed
because it become marked with highligthed snowflake.
So is your final purpose the alone solution to delete intermediates
datasets ? And if I correctly understand, I must create a tool that
take all my deletable datasets as input and which will remove all of
these. In this case, the postJobAction "DeleteIntermediates" is not
usefull, is it ?
Thanks.
Julie
2014-09-23 14:15 GMT+02:00 Dannon Baker :
> Hi Julie!
>
> The action resolves at the completion time of the job it is attached to,
> deleting datasets of any other already-completed jobs in that workflow which
> are not marked as an output step (with a highlighted snowflake). This will
> *not* delete datasets of any job marked as an output.
>
> Perhaps the confusion is that they're also marked as 'hidden' since they are
> not output steps?
>
> The general use-case for this is to put it on one of the 'final' steps of a
> workflow (or multiple if you have a workflow with two long parallel tracks)
> to clean up and delete datasets from intermediate jobs (which have already
> completed) that you don't want to save as an output.
>
> -Dannon
>
>
>
> On Tue, Sep 23, 2014 at 4:03 AM, julie dubois wrote:
>>
>> Hi all,
>> I'm not sure how do this post-action act . I've been make some test
>> and it's very confused for me.
>>
>> First, can this post-action be used on output which are used on other
>> steps of the workflow ? if yes, I suppose that galaxy wait for end of
>> use of this output before deleting.
>>
>> Second, must I higlight the snowfalke of this output to permit its
>> deletion or must I keep the snowflake in grey ?
>>
>> I post this question in galaxy-dev because I've added this
>> post-action on several outputs in my workflow and it has had no effect
>> on my outputs. And when I open the .ga file which describe my
>> workflow, I've seen just one of this post-action in one output.
>>
>>
>> Thanks.
>>
>> Julie
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>
___
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[galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput
Hi all, I'm not sure how do this post-action act . I've been make some test and it's very confused for me. First, can this post-action be used on output which are used on other steps of the workflow ? if yes, I suppose that galaxy wait for end of use of this output before deleting. Second, must I higlight the snowfalke of this output to permit its deletion or must I keep the snowflake in grey ? I post this question in galaxy-dev because I've added this post-action on several outputs in my workflow and it has had no effect on my outputs. And when I open the .ga file which describe my workflow, I've seen just one of this post-action in one output. Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How can I populate a data_collection output ?
Hello John, Thank you for your answer. We shall thus wait. Julie 2014-07-29 22:43 GMT+02:00 David Kelly : > Hi John, > > Is there any documentation that explains how dataset collections work? I'd > like to learn more about it. > > Thanks, > David > > > On Tue, Jul 29, 2014 at 3:20 PM, John Chilton wrote: >> >> Hello Julie, >> >> Right now Galaxy can implicitly create collections by running a tool >> that takes in a single input or a paired dataset over say a list of >> inputs or a list of paired inputs but tools cannot explicitly create >> dataset collections. I think Galaxy's current capabilities add a lot >> of useful functionality - but say tools that take a big input and >> split it into an arbitrary number of pieces or tools that >> normalize/summarize N inputs simultaneously and produce N outputs >> cannot be represented. A few people made some progress on this at the >> recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more >> people have made it clear that it is an important feature. >> >> Sorry. >> >> -John >> >> >> On Mon, Jul 28, 2014 at 11:47 AM, julie dubois wrote: >> > Hi all, >> > I'm working with data_collection as type of input in xml files. but I >> > use all the datasets of a collection to compute some results that I >> > want to push in a "data_collection" output. >> > I know how take each dataset of a data_collection input with my >> > script, like this : >> > >> > ... >> > for $f in $input >> > ... >> > >> > where $input is defined by > > collection_type=list... in the top of my xml file. >> > >> > But if my script produce some outputs (number of outputs not defined >> > in advance), how can I populate an output as a data_collection with my >> > shscript and how should I define this output in the xml ? >> > >> > Thanks >> > Julie >> > ___ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > http://lists.bx.psu.edu/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How can I populate a data_collection output ?
Hi all, I'm working with data_collection as type of input in xml files. but I use all the datasets of a collection to compute some results that I want to push in a "data_collection" output. I know how take each dataset of a data_collection input with my script, like this : ... for $f in $input ... where $input is defined by http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Jobs stay queued
Hi Hans-Rudolf. Yes, I have this error in my log file :"MySQL server has gone away"!!! So I changed the option database_engine_option_pool and it seems to work fine! Thanks a lot for your help. And for the information, when a job is queued on a local instance not in a cluster, when we restart the server, the job is crashed to the error state. Thanks again. julie 2014-07-23 14:25 GMT+02:00 Hans-Rudolf Hotz : > > > On 07/23/2014 02:13 PM, julie dubois wrote: >> >> I'm using a MySQL database !!! >> But may be such database-lock can appear because of my universe.ini >> configuration file. >> Here it's the lines concerning the database : >> >> database_engine_option_pool_size = 10 >> database_engine_option_max_overflow = 20 >> database_engine_option_pool_recycle = -1 >> database_engine_option_strategy = threadlocal >> >> >> Can one of these parameters be at the origin of my problem ? >> > > > we are also using MySQL, but we use the suggested setting: > > database_engine_option_pool_recycle = 7200 > > > though, i don't think this is related to your problem. Or did you get the > error: "MySQL server has gone away" in the galaxy log file? > > > >> >> If yes, when I'll restart Galaxy, the queued jobs will be in a staying >> state with the capacity to become in a running state ? >> Or they will be in error state and I should restart the process as new >> jobs ? > > > I don't know, I don't have enough experience with queued workflow jobs and > what is happening with them during a re-start. I am sorry, I can't be of > much further help. Maybe someone else on the list? > > Hans-Rudolf > > > > >> >> >> Thanks. >> >> Julie >> >> 2014-07-23 12:55 GMT+02:00 Hans-Rudolf Hotz : >>> >>> >>> >>> On 07/23/2014 12:05 PM, julie dubois wrote: >>>> >>>> >>>> Hi Hans-Rudolf, >>>> Thanks for your answer. >>>> I've launched lot of jobs since monday. And some jobs were finished >>>> and some jobs never started. >>>> In "Manage jobs" I can see jobs queued because they need inputs which >>>> are queued, so I think it's normal. >>>> >>>> But other jobs are described like this : >>>> >>>> 9554 user_login 0 hours agosamtools_flagstatnew23199 >>>> ok, 23243 okNoneNoneNone >>>> The two necessary inputs for this job (23199 and 2343) are ok and the >>>> job doesn't run. >>>> >>>> >>>> Another mysterious line is : >>>> >>>> 9561 user_login0 hours ago fastqc new Unable to >>>> determine inputs None NoneNone >>>> >>>> After check this job in my history, I'm sure that the input of this >>>> job is green and really available. Why can galaxy not determine inputs >>>> ? >>>> Finally, in "Manage Jobs" there are only jobs queued. No jobs running. >>>> >>>> Any idea ? >>> >>> >>> >>> I have one suspicion: >>> >>> which database are you using? >>> If you are just using the built in SQlite you might have run in a >>> database-lock? Because you have submitted too many jobs at once? >>> >>> In this case, I guess, the only way to recover is to re-start... >>> >>> Hans-Rudolf >>> >>> >>> >>>> Thanks >>>> Julie >>>> >>>> 2014-07-23 11:35 GMT+02:00 Hans-Rudolf Hotz : >>>>> >>>>> >>>>> Hi Julie >>>>> >>>>> Are there any jobs running at all? What do you get when you click on >>>>> "Manage jobs" in the admin menu? Maybe you have some old jobs >>>>> 'running' >>>>> which are now blocking your queue? >>>>> >>>>> Hans-Rudolf >>>>> >>>>> >>>>> >>>>> On 07/23/2014 11:14 AM, julie dubois wrote: >>>>>> >>>>>> >>>>>> >>>>>> Hi all, >>>>>> I've seen several posts for jobs which stay queued and never start >>>>>> with an installation of galaxy on a cluster. >>>>>> But our installation is just a local instance of galaxy in 1 PC and I >>>>>> have more than 100 jobs which stay queued and never start. >>>>>> >>>>>> How can I debug this problem (my version of galaxy is the latest >>>>>> 2june2014). >>>>>> >>>>>> And is it possible to run those jobs without restart galaxy because it >>>>>> would be very long to rerun each job manually after reloading galaxy. >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Julie >>>>>> ___ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> http://lists.bx.psu.edu/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Jobs stay queued
I'm using a MySQL database !!! But may be such database-lock can appear because of my universe.ini configuration file. Here it's the lines concerning the database : database_engine_option_pool_size = 10 database_engine_option_max_overflow = 20 database_engine_option_pool_recycle = -1 database_engine_option_strategy = threadlocal Can one of these parameters be at the origin of my problem ? If yes, when I'll restart Galaxy, the queued jobs will be in a staying state with the capacity to become in a running state ? Or they will be in error state and I should restart the process as new jobs ? Thanks. Julie 2014-07-23 12:55 GMT+02:00 Hans-Rudolf Hotz : > > > On 07/23/2014 12:05 PM, julie dubois wrote: >> >> Hi Hans-Rudolf, >> Thanks for your answer. >> I've launched lot of jobs since monday. And some jobs were finished >> and some jobs never started. >> In "Manage jobs" I can see jobs queued because they need inputs which >> are queued, so I think it's normal. >> >> But other jobs are described like this : >> >> 9554 user_login 0 hours agosamtools_flagstatnew23199 >> ok, 23243 okNoneNoneNone >> The two necessary inputs for this job (23199 and 2343) are ok and the >> job doesn't run. >> >> >> Another mysterious line is : >> >> 9561 user_login0 hours ago fastqc new Unable to >> determine inputs None NoneNone >> >> After check this job in my history, I'm sure that the input of this >> job is green and really available. Why can galaxy not determine inputs >> ? >> Finally, in "Manage Jobs" there are only jobs queued. No jobs running. >> >> Any idea ? > > > I have one suspicion: > > which database are you using? > If you are just using the built in SQlite you might have run in a > database-lock? Because you have submitted too many jobs at once? > > In this case, I guess, the only way to recover is to re-start... > > Hans-Rudolf > > > >> Thanks >> Julie >> >> 2014-07-23 11:35 GMT+02:00 Hans-Rudolf Hotz : >>> >>> Hi Julie >>> >>> Are there any jobs running at all? What do you get when you click on >>> "Manage jobs" in the admin menu? Maybe you have some old jobs 'running' >>> which are now blocking your queue? >>> >>> Hans-Rudolf >>> >>> >>> >>> On 07/23/2014 11:14 AM, julie dubois wrote: >>>> >>>> >>>> Hi all, >>>> I've seen several posts for jobs which stay queued and never start >>>> with an installation of galaxy on a cluster. >>>> But our installation is just a local instance of galaxy in 1 PC and I >>>> have more than 100 jobs which stay queued and never start. >>>> >>>> How can I debug this problem (my version of galaxy is the latest >>>> 2june2014). >>>> >>>> And is it possible to run those jobs without restart galaxy because it >>>> would be very long to rerun each job manually after reloading galaxy. >>>> >>>> Thanks. >>>> >>>> Julie >>>> ___ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Jobs stay queued
Hi Hans-Rudolf, Thanks for your answer. I've launched lot of jobs since monday. And some jobs were finished and some jobs never started. In "Manage jobs" I can see jobs queued because they need inputs which are queued, so I think it's normal. But other jobs are described like this : 9554 user_login 0 hours agosamtools_flagstatnew23199 ok, 23243 okNoneNoneNone The two necessary inputs for this job (23199 and 2343) are ok and the job doesn't run. Another mysterious line is : 9561 user_login0 hours ago fastqc new Unable to determine inputs None NoneNone After check this job in my history, I'm sure that the input of this job is green and really available. Why can galaxy not determine inputs ? Finally, in "Manage Jobs" there are only jobs queued. No jobs running. Any idea ? Thanks Julie 2014-07-23 11:35 GMT+02:00 Hans-Rudolf Hotz : > Hi Julie > > Are there any jobs running at all? What do you get when you click on > "Manage jobs" in the admin menu? Maybe you have some old jobs 'running' > which are now blocking your queue? > > Hans-Rudolf > > > > On 07/23/2014 11:14 AM, julie dubois wrote: >> >> Hi all, >> I've seen several posts for jobs which stay queued and never start >> with an installation of galaxy on a cluster. >> But our installation is just a local instance of galaxy in 1 PC and I >> have more than 100 jobs which stay queued and never start. >> >> How can I debug this problem (my version of galaxy is the latest >> 2june2014). >> >> And is it possible to run those jobs without restart galaxy because it >> would be very long to rerun each job manually after reloading galaxy. >> >> Thanks. >> >> Julie >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Jobs stay queued
Hi all, I've seen several posts for jobs which stay queued and never start with an installation of galaxy on a cluster. But our installation is just a local instance of galaxy in 1 PC and I have more than 100 jobs which stay queued and never start. How can I debug this problem (my version of galaxy is the latest 2june2014). And is it possible to run those jobs without restart galaxy because it would be very long to rerun each job manually after reloading galaxy. Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] moving tool-data : no build genome retrieve
Hi all, I'm moving the directory "tool-data" in other partition than galaxy-dist. I've set the tool-data-path in universe.ini to this new location. So, the indexes used by bowtie for example are retrieve without problem. But no build genome are available when we upload dataset or whit the pencil interface. Is there anoter file to configure the path of tool-data ? Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ImportError: No module named galaxy_utils.sequence.fastq
Thanks! Actually it's not for the toolshed, for the moment... But I'm very intereseted by details to install it into a virtualenv. Thank you. Julie 2014-07-07 16:16 GMT+02:00 John Chilton : > Ahhh - I get it now. Galaxy only adds itself to the PYTHONPATH if it > can infer it is running a Python script (i.e. the command block starts > with python or a Python interpreter is used). > > If you are building a tool for the tool shed - it would be best to > setup a tool dependency on the galaxy_sequence_utils package - this > would force every execution of the tool to have these utilities on > your PYTHONPATH. But since you are hard-encoding paths - it looks like > you are tailoring your Galaxy instance to your local environment. In > this case an easy hack is to just setup that dependency globally for > the system: > > sudo easy_install > http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.0.tgz > > If you are setting up Galaxy env.sh files this can be installed into a > virtualenv instead - which is a better practice - let me know if you > are interested and I can send details. > > -John > > > > > On Mon, Jul 7, 2014 at 4:02 AM, julie dubois wrote: >> Hi John, >> >> As I specified it in the "edit" of my first message, I have this error >> only if I run groomer with a command line in another xml file >> surrounding by other command. When I run groomer alone with the >> original xml, it works fine, so no problem with the PYTHONPATH. >> But when I use this : >> >> #if $fastq_format == "illumina" >> blabla_No_python_command >> #else >> python /data/galaxy-dist/tools/fastq/fastq_groomer.py >> 'tmp.fastqcssanger' 'cssanger' '$output' 'illumina' 'ascii' >> 'dont_summarize_input' >> #end if >> >> >> It doesn't work. >> >> I've checked the files contained in job_working_directory. A shell >> script is generated for my job and it begin with these lines : >> >> #!/bin/sh >> >> GALAXY_SLOTS="1"; export GALAXY_SLOTS; >> export GALAXY_SLOTS >> GALAXY_LIB="None" >> if [ "$GALAXY_LIB" != "None" ]; then >> if [ -n "$PYTHONPATH" ]; then >> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" >> else >> PYTHONPATH="$GALAXY_LIB" >> fi >> export PYTHONPATH >> fi >> >> >> >> So, with the run of groomer alone the line GALAXY_LIB is equal to >> "/data/galaxy/galaxy-dist/lib", but here with the run of groomer with >> a command line with another job the GALAXY_LIB is set to "None"!!! >> I don't understand why. >> >> For the moment, to surround the problem, I've explicitly specified the >> GALAXY_LIB path int the xml command before the command line wich run >> python fastq_groomer.py and it works but I'm aware that is not >> beautiful. >> >> Finally I'm using a local jobrunner. >> >> Thanks for your help >> Julie >> >> P.S : we use such command because we build a workflow where the >> quality format of the fastq must be invisible for the users. >> >> 2014-07-03 19:48 GMT+02:00 John Chilton : >>> Hello Julie, >>> >>> This is odd - sorry. >>> >>> I might be worth uninstalling and re-installing this in the tool >>> shed admin options - in particular ensure you install tool >>> dependencies and that this installation process succeeds. >>> >>> Otherwise - it might be worth trying to put some debug statements >>> in the fastq groomer tool to try to track down the problem. Here >>> (https://gist.github.com/jmchilton/2d61f7ab81d99a0f02fc) is a diff to >>> have that tool write out the run-time value PYTHONPATH to Galaxy's >>> home directory - it might be worth running a job, finding the output, >>> setting PYTHONPATH to that value on the compute node and attempting to >>> just import it directly. >>> >>> cd $HOME; python -c "import galaxy.sequences.fastq" >>> >>> Out of curiosity - what job runner are you using (local, DRMAA, etc...)? >>> >>> -John >>> >>> On Tue, Jul 1, 2014 at 4:50 AM, julie dubois wrote: >>>> Hi, >>>> I've this error message when I run groomer. >>>> >>>> My local instance of galaxy runs on a python vir
Re: [galaxy-dev] ImportError: No module named galaxy_utils.sequence.fastq
Hi John, As I specified it in the "edit" of my first message, I have this error only if I run groomer with a command line in another xml file surrounding by other command. When I run groomer alone with the original xml, it works fine, so no problem with the PYTHONPATH. But when I use this : #if $fastq_format == "illumina" blabla_No_python_command #else python /data/galaxy-dist/tools/fastq/fastq_groomer.py 'tmp.fastqcssanger' 'cssanger' '$output' 'illumina' 'ascii' 'dont_summarize_input' #end if It doesn't work. I've checked the files contained in job_working_directory. A shell script is generated for my job and it begin with these lines : #!/bin/sh GALAXY_SLOTS="1"; export GALAXY_SLOTS; export GALAXY_SLOTS GALAXY_LIB="None" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi So, with the run of groomer alone the line GALAXY_LIB is equal to "/data/galaxy/galaxy-dist/lib", but here with the run of groomer with a command line with another job the GALAXY_LIB is set to "None"!!! I don't understand why. For the moment, to surround the problem, I've explicitly specified the GALAXY_LIB path int the xml command before the command line wich run python fastq_groomer.py and it works but I'm aware that is not beautiful. Finally I'm using a local jobrunner. Thanks for your help Julie P.S : we use such command because we build a workflow where the quality format of the fastq must be invisible for the users. 2014-07-03 19:48 GMT+02:00 John Chilton : > Hello Julie, > > This is odd - sorry. > > I might be worth uninstalling and re-installing this in the tool > shed admin options - in particular ensure you install tool > dependencies and that this installation process succeeds. > > Otherwise - it might be worth trying to put some debug statements > in the fastq groomer tool to try to track down the problem. Here > (https://gist.github.com/jmchilton/2d61f7ab81d99a0f02fc) is a diff to > have that tool write out the run-time value PYTHONPATH to Galaxy's > home directory - it might be worth running a job, finding the output, > setting PYTHONPATH to that value on the compute node and attempting to > just import it directly. > > cd $HOME; python -c "import galaxy.sequences.fastq" > > Out of curiosity - what job runner are you using (local, DRMAA, etc...)? > > -John > > On Tue, Jul 1, 2014 at 4:50 AM, julie dubois wrote: >> Hi, >> I've this error message when I run groomer. >> >> My local instance of galaxy runs on a python virtualenv (python 2.7) >> and I have make the latest update with : hg pull -u. >> >> I've verified and this library is present in my >> galaxy-dist/lib/galaxy_utils/sequence directory. >> >> I've found no other idea than the update on this forum to run groomer >> correctly, any other idea ? >> >> Thanks. >> Julie >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bug with workflow
Hi, Thanks for your answer. I've no failed job in my history. I've checked the workflow and it is the same as before update. But your answer highlight another point ! The tool I use in my final step has been modified after update of galaxy and not tested alone. When I've tested this tool alone, I've seen this error in the middle panel "output" not found (it was a variable name which have been changed after update !!!). It's the first time that I have such error with no entry in history preventing a check of stderr and stdout, so I didn't think that it can be come from my tool. Thanks for your help. Julie 2014-07-07 2:22 GMT+02:00 John Chilton : > There is likely a failed job somewhere in your history? Can you look > at that for details - standard out, standard error, etc...? > > Can you open the workflow in the workflow editor and see if it still > looks the same as before the update? > > Also, can you export the workflow and send it to me? > > Thanks, > -John > > On Thu, Jul 3, 2014 at 2:20 AM, julie dubois wrote: >> Hi all, >> I've a bug with the use of workflow. I've created my own workflow and >> since the latest update the workflow can be launched correctly but not >> completely!!! >> >> The first steps works with outputs on history, a job runs in >> job_working_directory for each of these steps. But for my final step : >> no job begin in job_working_directory so no data in history because >> the jobs don't exist. >> >> In my workflow the outputs are selected to be not hidden and the final >> step is connected with other steps. >> >> Any other one have this problem ? >> >> Thanks. >> >> Julie >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Bug with workflow
Hi all, I've a bug with the use of workflow. I've created my own workflow and since the latest update the workflow can be launched correctly but not completely!!! The first steps works with outputs on history, a job runs in job_working_directory for each of these steps. But for my final step : no job begin in job_working_directory so no data in history because the jobs don't exist. In my workflow the outputs are selected to be not hidden and the final step is connected with other steps. Any other one have this problem ? Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] ImportError: No module named galaxy_utils.sequence.fastq
Hi, I've this error message when I run groomer. My local instance of galaxy runs on a python virtualenv (python 2.7) and I have make the latest update with : hg pull -u. I've verified and this library is present in my galaxy-dist/lib/galaxy_utils/sequence directory. I've found no other idea than the update on this forum to run groomer correctly, any other idea ? Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Dataset_Collections : an example of code for a tool ?
Thanks a lot !!! I think other questions will appear with the use of collections in workflows, but it will be an other story :) Julie 2014-06-04 17:00 GMT+02:00 John Chilton : > Hello Julie, > > Thanks for your interest in dataset collections! Good luck with your > experiments and sorry about the bumps in road you will experience - > these are early days :). Here are the modified tools from the example: > > https://gist.github.com/jmchilton/b6773c8433224ea7ed78 > > These examples may not make sense because the example in the > presentation is highly contrived. There are some equally contrived - > but much simpler tools (to visualize, test the concepts) - in Galaxy's > test tools directory > ( > https://bitbucket.org/galaxy/galaxy-central/src/default/test/functional/tools/ > ) > see collection_mixed_param.xml, collection_nested_test.xml, and > collection_paired_test.xml. > > Hope this helps. > > -John > > On Wed, Jun 4, 2014 at 9:40 AM, julie dubois wrote: > > Hi, > > Your latest update is very exciting with the introduction of > > Dataset_Collections!!! > > It's very useful for us . I've been testing it in a new install of Galaxy > > and I can create a Dataset_Collection in my history. > > But with the reading of trello cards and this presentation : > > > https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhufIp-ysxYA/edit#slide=id.g33c342448_143 > > I've not yet found how to code a tool to use this collection and/or > unique > > dataset. > > > > Is it possible to have the bowtie2 version (and or Merge Bam) with these > 2 > > possibilities to have an example? And how can I see the icons in the > > formular which allow to switch between the use of unique dataset and the > use > > of dataset collection, like is presented in the presentation ? > > > > Thanks. > > > > Julie > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Dataset_Collections : an example of code for a tool ?
Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation : https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhufIp-ysxYA/edit#slide=id.g33c342448_143 I've not yet found how to code a tool to use this collection and/or unique dataset. Is it possible to have the bowtie2 version (and or Merge Bam) with these 2 possibilities to have an example? And how can I see the icons in the formular which allow to switch between the use of unique dataset and the use of dataset collection, like is presented in the presentation ? Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Dataset_Collections : an example of code for a tool ?
Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhufIp-ysxYA/edit#slide=id.g33c342448_143 I've not yet found how to code a tool to ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Display history.id in History Panel
Hi all, In a local instance of Galaxy, I rename all outputs of my users and redirect their in a directory named with their usermail galaxy and then in a directory named with the history.id. To help them to retrieve their datasets, I want to display the history.idat the top of the History left panel, for example near the name of the history. Can you say me which file(s) should I modify and how to display this information ? Thanks a lot. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Local data for encode tools
Hi all, I want to use the encode tools as "random intervals" in my local instance of galaxy cistrome. I have the xml file and the py file which can run the tool, but it required any local data. These data are referenced in tool-data/regions.loc but I've not found where can I procure the bed which are referenced in this file. Have you any idea to find them or to build them ? Or just any example of their format, may be I can reproduce them with other data. And for the future, is there a precise web page for admin which references all ways to transfer useful local data? Thanks a lot. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Import history from web server to local server
THANKS a lot It works. It's a very big advance for us. Thanks again. Julie 2013/2/7 Jeremy Goecks > This means the history is still being compressed; large histories can take > a long time to compressed, so you'll have to be patient and check back > periodically to see when the history is ready for download. > > Best, > J. > > On Feb 7, 2013, at 4:02 AM, julie dubois wrote: > > Sorry for my stupid ask but when I click on the link provide by the option > "Export to File", I'm redirected on web page which shows me this message : > Still exporting history MyHistory;pleas check back soon. Link: > http://cistrome.org/ap/history/export_archive?id=### > > I have no possibility to download the history! What is the problem? I have > certainly mis-understanded your explaination. > Thanks. > julie > > 2013/2/6 Jeremy Goecks > >> Unfortunately using wget won't work in this case. The reason you have >> access to the history is your Galaxy cookie, which isn't shared with >> wget/curl. >> >> You'll need to click on the export link in your Web browser to download >> the history to your local computer and then move it to a local server. >> >> Best, >> J. >> >> On Feb 6, 2013, at 12:07 PM, julie dubois wrote: >> >> Thanks! >> Just one ask : How can I download this compressed history : is it the >> same that : >> wget url_of_exported_history >> and copy the file from this command in a local server ? >> Because this file is not an archive but a text file with html code >> >> thanks again. >> Julie >> >> 2013/2/6 Jeremy Goecks >> >>> Ah, I see the issue: the Cistrome instance cannot be used anonymously >>> (without login). It's not possible for one Galaxy instance to work with >>> another instance's history because instances work with objects anonymously >>> rather than using login credentials. >>> >>> For now, you can download/copy the compressed history to a >>> Web-accessible location (e.g. local web server, Dropbox) and import the >>> history from that location. We'll look into improving this in the future. >>> >>> Best, >>> J. >>> >>> On Feb 6, 2013, at 11:10 AM, julie dubois wrote: >>> >>> Hi, thanks for your help. >>> I've tested your procedure and it doesn't work. I have the same error. >>> >>> Sorry and thanks for the creation of the card. >>> Julie >>> >>> 2013/2/6 Jeremy Goecks >>> >>>> This is likely a permissions issue: importing your history into another >>>> Galaxy instance requires the history to be accessible. Here's a solution >>>> that, while ugly, should work: >>>> >>>> (1) Make the history accessible by going to Share/Publish and clicking >>>> the option to make it accessible. >>>> (2) Export your history again. >>>> (3) Use the history URL to import to another instance. >>>> >>>> I've created a card for enhancements to this feature that will make >>>> this process easier in the future. >>>> >>>> https://trello.com/c/qCfAWeYU >>>> >>>> Best, >>>> J >>>> >>>> >>>> On Feb 6, 2013, at 5:00 AM, julie dubois wrote: >>>> >>>> Hi all, >>>> I'm trying to import an history from the web server to my local server. >>>> First I've chosen "Export to File" in the history menu and I've seen a >>>> message with an url. >>>> Second in my local server I've created a new history and I chosen >>>> "Import from File" in my new history menu. >>>> I've pasted the url in the formular and A message says : >>>> "Importing history from ' >>>> http://cistrome.org/ap/history/export_archive?id='. >>>> This history will be visible when the import is complete" >>>> >>>> But there is nothing in my new history and it seems that no operation >>>> is running!!! >>>> >>>> Is it normal? >>>> Another idea to transfer an hitory and his datasets in another history? >>>> Thanks. >>>> julie >>>> ___ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>>> >>>> >>>> >>> >>> >> >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Import history from web server to local server
Sorry for my stupid ask but when I click on the link provide by the option "Export to File", I'm redirected on web page which shows me this message : Still exporting history MyHistory;pleas check back soon. Link: http://cistrome.org/ap/history/export_archive?id=### I have no possibility to download the history! What is the problem? I have certainly mis-understanded your explaination. Thanks. julie 2013/2/6 Jeremy Goecks > Unfortunately using wget won't work in this case. The reason you have > access to the history is your Galaxy cookie, which isn't shared with > wget/curl. > > You'll need to click on the export link in your Web browser to download > the history to your local computer and then move it to a local server. > > Best, > J. > > On Feb 6, 2013, at 12:07 PM, julie dubois wrote: > > Thanks! > Just one ask : How can I download this compressed history : is it the same > that : > wget url_of_exported_history > and copy the file from this command in a local server ? > Because this file is not an archive but a text file with html code > > thanks again. > Julie > > 2013/2/6 Jeremy Goecks > >> Ah, I see the issue: the Cistrome instance cannot be used anonymously >> (without login). It's not possible for one Galaxy instance to work with >> another instance's history because instances work with objects anonymously >> rather than using login credentials. >> >> For now, you can download/copy the compressed history to a Web-accessible >> location (e.g. local web server, Dropbox) and import the history from that >> location. We'll look into improving this in the future. >> >> Best, >> J. >> >> On Feb 6, 2013, at 11:10 AM, julie dubois wrote: >> >> Hi, thanks for your help. >> I've tested your procedure and it doesn't work. I have the same error. >> >> Sorry and thanks for the creation of the card. >> Julie >> >> 2013/2/6 Jeremy Goecks >> >>> This is likely a permissions issue: importing your history into another >>> Galaxy instance requires the history to be accessible. Here's a solution >>> that, while ugly, should work: >>> >>> (1) Make the history accessible by going to Share/Publish and clicking >>> the option to make it accessible. >>> (2) Export your history again. >>> (3) Use the history URL to import to another instance. >>> >>> I've created a card for enhancements to this feature that will make this >>> process easier in the future. >>> >>> https://trello.com/c/qCfAWeYU >>> >>> Best, >>> J >>> >>> >>> On Feb 6, 2013, at 5:00 AM, julie dubois wrote: >>> >>> Hi all, >>> I'm trying to import an history from the web server to my local server. >>> First I've chosen "Export to File" in the history menu and I've seen a >>> message with an url. >>> Second in my local server I've created a new history and I chosen >>> "Import from File" in my new history menu. >>> I've pasted the url in the formular and A message says : >>> "Importing history from ' >>> http://cistrome.org/ap/history/export_archive?id='. >>> This history will be visible when the import is complete" >>> >>> But there is nothing in my new history and it seems that no operation is >>> running!!! >>> >>> Is it normal? >>> Another idea to transfer an hitory and his datasets in another history? >>> Thanks. >>> julie >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> >>> >> >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Import history from web server to local server
Thanks! Just one ask : How can I download this compressed history : is it the same that : wget url_of_exported_history and copy the file from this command in a local server ? Because this file is not an archive but a text file with html code thanks again. Julie 2013/2/6 Jeremy Goecks > Ah, I see the issue: the Cistrome instance cannot be used anonymously > (without login). It's not possible for one Galaxy instance to work with > another instance's history because instances work with objects anonymously > rather than using login credentials. > > For now, you can download/copy the compressed history to a Web-accessible > location (e.g. local web server, Dropbox) and import the history from that > location. We'll look into improving this in the future. > > Best, > J. > > On Feb 6, 2013, at 11:10 AM, julie dubois wrote: > > Hi, thanks for your help. > I've tested your procedure and it doesn't work. I have the same error. > > Sorry and thanks for the creation of the card. > Julie > > 2013/2/6 Jeremy Goecks > >> This is likely a permissions issue: importing your history into another >> Galaxy instance requires the history to be accessible. Here's a solution >> that, while ugly, should work: >> >> (1) Make the history accessible by going to Share/Publish and clicking >> the option to make it accessible. >> (2) Export your history again. >> (3) Use the history URL to import to another instance. >> >> I've created a card for enhancements to this feature that will make this >> process easier in the future. >> >> https://trello.com/c/qCfAWeYU >> >> Best, >> J >> >> >> On Feb 6, 2013, at 5:00 AM, julie dubois wrote: >> >> Hi all, >> I'm trying to import an history from the web server to my local server. >> First I've chosen "Export to File" in the history menu and I've seen a >> message with an url. >> Second in my local server I've created a new history and I chosen "Import >> from File" in my new history menu. >> I've pasted the url in the formular and A message says : >> "Importing history from ' >> http://cistrome.org/ap/history/export_archive?id='. This >> history will be visible when the import is complete" >> >> But there is nothing in my new history and it seems that no operation is >> running!!! >> >> Is it normal? >> Another idea to transfer an hitory and his datasets in another history? >> Thanks. >> julie >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Import history from web server to local server
Hi, thanks for your help. I've tested your procedure and it doesn't work. I have the same error. Sorry and thanks for the creation of the card. Julie 2013/2/6 Jeremy Goecks > This is likely a permissions issue: importing your history into another > Galaxy instance requires the history to be accessible. Here's a solution > that, while ugly, should work: > > (1) Make the history accessible by going to Share/Publish and clicking the > option to make it accessible. > (2) Export your history again. > (3) Use the history URL to import to another instance. > > I've created a card for enhancements to this feature that will make this > process easier in the future. > > https://trello.com/c/qCfAWeYU > > Best, > J > > > On Feb 6, 2013, at 5:00 AM, julie dubois wrote: > > Hi all, > I'm trying to import an history from the web server to my local server. > First I've chosen "Export to File" in the history menu and I've seen a > message with an url. > Second in my local server I've created a new history and I chosen "Import > from File" in my new history menu. > I've pasted the url in the formular and A message says : > "Importing history from ' > http://cistrome.org/ap/history/export_archive?id='. This > history will be visible when the import is complete" > > But there is nothing in my new history and it seems that no operation is > running!!! > > Is it normal? > Another idea to transfer an hitory and his datasets in another history? > Thanks. > julie > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Import history from web server to local server
Hi all, I'm trying to import an history from the web server to my local server. First I've chosen "Export to File" in the history menu and I've seen a message with an url. Second in my local server I've created a new history and I chosen "Import from File" in my new history menu. I've pasted the url in the formular and A message says : "Importing history from ' http://cistrome.org/ap/history/export_archive?id='. This history will be visible when the import is complete" But there is nothing in my new history and it seems that no operation is running!!! Is it normal? Another idea to transfer an hitory and his datasets in another history? Thanks. julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] updates with hg incoming
Hi all, I wondered if when we make an update via hh it erased the previous files or if that added the modifications to files. Because I've modified several scripts to customize my local galaxy and I don't want that these modifications desappear with an update. Thanks. julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Import error : no module named ...
Hi all, Happy new year! I have western mysteries that I cannot resolve. I have a local instance of galaxy and while this instance run correctly since several hours or days, suddenly the jobs fail and this error appears : Import error : no module named CistromeAP.jianlib.inout CistromeAP is the name of my main directory for galaxy and it contains the sub directory jianlib with the script inout.py. Tha application which runs with this module runs correctly for several jobs and for a mysterious reason, a next job don't run because it cannot find the scripts. This error appears with different applications and at different time of using of galaxy. Sometimes even, it appears just after the launching of galaxy!!! Is it a problem with my server apache and why ? Have you a test to know where come the problem from? Thanks. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Where is the xml file of "edit attribute"? and history name
Hi, I've redirected all of my outputs in an other directory with my own names after each run of tools.. But when the users want to rename their datasets on the history, I would want that this change occurs on my output files already register in the computer. So where can I find the xml file of the function "edit attribute" and from this file, can I take the real name of my output file before the change? Another question is about the history name : because the users use several history, I need to know how call the variable of the history name ; for exemple if an output variable is $output, the history name of this variable is : $output.history_name ? or $output.history.name? or if this name is not accessible in this way, may be the history id ? In my first step when I rename an output, I take the $output.hid which indicate me the number of the dataset in an history. But I've not found the name of this history. Thanks Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] output name of downloaded datasets
Hello, My goal is to introduce, in the xml file of one tool like MACS for example, a supplementary command to redirect the output in another directory (+ creating link between this and the directory of galaxy outputs). But I want to rename my output with the same name that the downloading tools create in this way : GALAXY-NumOfDatasetInHistory[NameOfInput].bed And I don't find where this downloading tool is and so I don't find how create this name. Thanks. julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Error with Heatmap : need bx-python while it's installed
Hi all, I have a problem with one of applications of galaxy-cistrome : when I run the application Heatmap, it didn't work and the log says me : "need bx-python" It's very clear. but on another pc with same installation, Heatmap run and furthermore bx-python is installed with your procedure : in galaxy-env mode with easy_install bx-python and no error message appear during this installation. Any idea of where can the problem come ? Thanks. julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Load Balancer config doesn't work
Hi, After several post in an Apache Forum, I've solve any problem of my apache configuration to enable load balancer configuration. It seems work but when I launch my galaxy application, I arrive in this web page : Service temporarily Unavailable And my log apache shows this : [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8083 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8082 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8081 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8080 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) It means that galaxy doesn't listen the port 8080, 8081 ... I think it's my run.sh which cannot read my universe_wsgi.ini correctly. Because if it could read correctly, in my terminal I could see this type of line : Handling web0 with log file web0.log...Entering daemon mode... Now, Idon't see that! after the command GALAXY_RUN_ALL=1 sh run.sh --daemon, I just see : Entering Daemon mode. So in my view, it's not an Apache problem but a shell script galaxy problem. Somedy has already met this problem ? Have you a solution ? Thank you. Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Avoid to download output files
It works !!! I've changed the extension of output file of an application. But in Galaxy, it's referenced over the old file with .dat in history, so if we want to re-use this file with other tool it's not the best way to change this extension after the run of tool. If I could change the extension before the chargement in history, that would be perfect. But I suppose it's not possible. I'm already satisfied of the possibility I've discover with the modification of xml files. Thank you for your help Julie 2012/5/24 Peter Cock > On Thu, May 24, 2012 at 3:27 PM, julie dubois wrote: > > Ok I've tried to add my script perl in the command line with semi-colon. > > It's work > > But this script sets in entry the variable $wigoutput of my file xml. But > > when I show it, it's not what I want; It's just the value : 1 . > > I think it's because the script of the application (macs) is called > before > > my script, the $wigoutput doesn't contain the good value when it stops. > > It is what I think, it's not possible to change the extension. > > > > Thank you for your attention and your answers > > Julie > > Well, yes, if you do this at the command line: > > cmdA; cmdB > > then cmdA is executed before cmdB. > > Try it yourself at the Unix/Linux prompt, e.g. > > date; ls > > compared to: > > ls; date > > If you want to run it first, try putting your script BEFORE the existing > entry in the tool XML's tag. > > Peter > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How must I configure Apache ?
Yes a follow this wiki but it doesn't work. I've tried to post too in apache forum because may be it's simply a problem with apache. thank you for your help. Julie 2012/5/24 Carlos Borroto > Glad it helped. > > About configuring Galaxy to use port 8080, other than what you are > already doing, checking for another process already using the port, I > wouldn't know what to recommend. > > About the balancing configuration, I haven't done it, so I don't have > much to help with that. I do think it should go in the virtual host > configuration file(default) and I don't think it should matter if you > put it before or after the rewrite rules. > > Are you following the instructions in?: > > http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling > > Regards, > Carlos > > On Mon, May 21, 2012 at 4:17 AM, julie dubois wrote: > > Hi, > > Thanks for your answer. > > Effectively it's not necessary on integrating Galaxy with a third party > > authentication system. > > I've integrated my configuration to the file "default" and it's work ! > > > > Just one remark. I've configured the file ports.conf with the line : > > "Listen 8080", and it didn't work! > > In fact, the shell says me that the galaxy port was already in use while > the > > command lsof -ti : 8080 showed no result. > > And when I delete the line "listen 8080" of my file ports.conf, Galaxy > work! > > Is it normal ? > > > > Finally, if I want tu use the proxy balancer lines like this (it is in > the > > hope to increase performances): > > > > Balancer member... > > ... > > > > > > must I add in default file (and before or after the rewrite rules?) or > in an > > other file ? > > > > Thank you in advance. > > Julie > > > > 2012/5/18 Carlos Borroto > >> > >> Hi Julie, > >> > >> Could you answer a couple of questions? > >> > >> First, are you interested on integrating Galaxy with a third party > >> authentication system? > >> > >> Second, do you expect heavy usage(I would say hundreds of concurrent > >> users) where you would need several Galaxy servers with the work load > >> balanced amount them?. Note even if you only have one Galaxy server, > >> you will still have several Apache processes running and you will be > >> able to serve multiple concurrent users without issue. Well at least > >> from the web server side of things, if you expect even a moderate > >> usage you should use a database back-end like PostgreSQL or MySQL. > >> > >> If the answer to these questions is no, all you need in a > >> Debian/Ubuntu system is to place this in > >> '/etc/apache2/sites-available/default' file between the > >> tags: > >> RewriteEngine on > >> RewriteRule ^/static/style/(.*) > >> /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] > >> RewriteRule ^/static/scripts/(.*) > >> /home/nate/galaxy-dist/static/scripts/packed/$1 [L] > >> RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L] > >> RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L] > >> RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L] > >> RewriteRule ^(.*) http://localhost:8080$1 [P] > >> > >> Even if the answer if yes to both questions, I would start with the > >> simpler setup first, get it working and then grow from there. > >> > >> Hope it helps, > >> Carlos > >> > >> On Fri, May 18, 2012 at 6:59 AM, julie dubois > wrote: > >> > Hi, > >> > First, Sorry but, I'm a newbie with Apache and my questions will > >> > certainly > >> > appear stupid. > >> > > >> > To configure apache2, I've followed this wiki : > >> > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy > >> > And I write these instructions : > >> > > >> > http://localhost:8080> > >> > Order deny,allow > >> > Allow from all > >> > > >> > RewriteEngine on > >> > > >> > # Define the authentication method > >> > AuthType Basic > >> > AuthName Galaxy > >> > AuthUserFile /home/nate/htpasswd > >> > Require valid-user > >> > # Take the $REMOTE_USER environment variable and set it as a > header >
Re: [galaxy-dev] Avoid to download output files
Ok I've tried to add my script perl in the command line with semi-colon. It's work But this script sets in entry the variable $wigoutput of my file xml. But when I show it, it's not what I want; It's just the value : 1 . I think it's because the script of the application (macs) is called before my script, the $wigoutput doesn't contain the good value when it stops. It is what I think, it's not possible to change the extension. Thank you for your attention and your answers Julie 2012/5/24 Jeremy Goecks > > > Thank you Jeremy, > > you answered partially. I would like insert a command, to launch my > script, in the script or in the xml files of my tools to force it to change > the extension of output files. > > But it seems impossible because my command perl after the command of > tool's script doesn't work in xml file. > > The key thing to know is that Galaxy creates a single command line when > running a tool, not a script. So, to add your command to a tool, you could > try adding a semi-colon as a separator and then your command. E.g. > > ...; python my_prog.py [inputs] > > > Best, > J. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Avoid to download output files
Thank you Jeremy, you answered partially. I would like insert a command, to launch my script, in the script or in the xml files of my tools to force it to change the extension of output files. But it seems impossible because my command perl after the command of tool's script doesn't work in xml file. I think, I will use your first proposition with symbolic links. Thank you. Julie 2012/5/24 Jeremy Goecks > Is it possible to change this with a simple change in a configuration file > or in a script file ? > > > No, they must be named as is for Galaxy to find them. You could, however, > create symbolic links to files and use an extension of your choice. > > Or, must I write my owner script, and if yes, how can I configure Galaxy > so that it launches it automatically after one application like MACS for > exemple which have a file configuration : macs.xml in the tools directory? > Because I've tried to add a line like this in this file : > mon scrip.pl > I've placed it after the line which launches the MACS script, > but my script seems not work. > > > It's not possible to launch Galaxy automatically on local files. You'll > need to upload the file to Galaxy and run the tool using the uploaded file > as input. > > Hopefully I answered your question; if not, can be more specific about > what you're trying to do? > > Best, > J. > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Avoid to download output files
Hi, I don't want dowload the output files which Galaxy generates, because I don't want to have them in double in my disk. I saw, that the output files are in file_path an I found them. But they have a .dat extension ! In your mailing-list archive I haven't found a solution to transform these extensions. Is it possible to change this with a simple change in a configuration file or in a script file ? Or, must I write my owner script, and if yes, how can I configure Galaxy so that it launches it automatically after one application like MACS for exemple which have a file configuration : macs.xml in the tools directory? Because I've tried to add a line like this in this file : mon scrip.pl I've placed it after the line which launches the MACS script, but my script seems not work. Thank you. julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Uploading problem
Thanks for your answer. I've solved the problem in another way : I've used Upload files from filesystem paths. It's very quick because it doesn't upload the files, just save the path where the data is! Thanks Julie 2012/5/22 Kelkar, Hemant > Are these problems cropping up because of possible system resource > limits being imposed on the user that is running galaxy? > > It may be worthwhile to check the /etc/login.conf (not sure that the > analogous file is in Ubuntu). Same may be true for Postgres ( > http://www.postgresql.org/docs/8.2/static/kernel-resources.html). > > ** ** > > --hk > > ** ** > > *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: > galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *J. Greenbaum > *Sent:* Tuesday, May 22, 2012 9:50 AM > *To:* julie dubois > *Cc:* galaxy-dev@lists.bx.psu.edu > *Subject:* Re: [galaxy-dev] Uploading problem > > ** ** > > Hi Julie, All, > > ** ** > > I have a similar problem on a test environment with a postgres backend. > The file that I'm uploading is a 50MB GTF file and it I'm getting the same > behavior. Any help would be appreciated. > > ** ** > > Thanks, > > ** ** > > Jason > > ** ** > > -- > > *Jason Greenbaum, Ph.D. > *Manager, Bioinformatics Core | jgb...@liai.org > La Jolla Institute for Allergy and Immunology > > ** ** > > ** ** > > ** ** > -- > > *From: *"julie dubois" > *To: *galaxy-dev@lists.bx.psu.edu > *Sent: *Tuesday, May 22, 2012 12:12:06 AM > *Subject: *[galaxy-dev] Uploading problem > > Hi, > I test a production environnement of Galaxy with apache proxy and mysql > database. > It work, but when I upload a file (it's not very big : 460 Mo), Galaxy > says that dataset is uploading and it has runned since yesterday and it's > not finish! > Where can the problem be ? Is it an installation problem or a material > limitation : it's run in a machine with 8 Go RAM and 4 cores processor. > > Thank you > > Julie > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > ** ** > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Uploading problem
Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor. Thank you Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] How can I connect to galaxy with multiple handlers and Galaxy performances
Hi, I've follow the instruction of this wiki : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling And when I ran the command : GALAXY_RUN_ALL=1 sh run.sh --daemon I've just obtain this answer in the terminal : Entering daemon mode without this type of line : Handling web0 with log file web0.log First : is it normal and is my apache configuration right : In my Default file I add ... after my rewrite rules and it replace the instructions :http://localhost:8080>... Second : how can I connect in my browser to Galaxy, because I've tried http://localhost:8080/galaxy and http://localhost:8079/galaxy and it didn't work, the browser says me : unable to connect I set this configuration because I want to increase the performances of Galaxy. in fact when I upload a file, with your web server, it run in 20 minutes and with my server it don't finish after 1 hour! Is it normal? Thank you for your attention. julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How must I configure Apache ?
Hi,
Thanks for your answer.
Effectively it's not necessary on integrating Galaxy with a third party
authentication system.
I've integrated my configuration to the file "default" and it's work !
Just one remark. I've configured the file ports.conf with the line :
"Listen 8080", and it didn't work!
In fact, the shell says me that the galaxy port was already in use while
the command lsof -ti : 8080 showed no result.
And when I delete the line "listen 8080" of my file ports.conf, Galaxy work!
Is it normal ?
Finally, if I want tu use the proxy balancer lines like this (it is in the
hope to increase performances):
Balancer member...
...
must I add in default file (and before or after the rewrite rules?) or in
an other file ?
Thank you in advance.
Julie
2012/5/18 Carlos Borroto
> Hi Julie,
>
> Could you answer a couple of questions?
>
> First, are you interested on integrating Galaxy with a third party
> authentication system?
>
> Second, do you expect heavy usage(I would say hundreds of concurrent
> users) where you would need several Galaxy servers with the work load
> balanced amount them?. Note even if you only have one Galaxy server,
> you will still have several Apache processes running and you will be
> able to serve multiple concurrent users without issue. Well at least
> from the web server side of things, if you expect even a moderate
> usage you should use a database back-end like PostgreSQL or MySQL.
>
> If the answer to these questions is no, all you need in a
> Debian/Ubuntu system is to place this in
> '/etc/apache2/sites-available/default' file between the
> tags:
> RewriteEngine on
> RewriteRule ^/static/style/(.*)
> /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/static/scripts/(.*)
> /home/nate/galaxy-dist/static/scripts/packed/$1 [L]
> RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
> RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
> Even if the answer if yes to both questions, I would start with the
> simpler setup first, get it working and then grow from there.
>
> Hope it helps,
> Carlos
>
> On Fri, May 18, 2012 at 6:59 AM, julie dubois wrote:
> > Hi,
> > First, Sorry but, I'm a newbie with Apache and my questions will
> certainly
> > appear stupid.
> >
> > To configure apache2, I've followed this wiki :
> > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
> > And I write these instructions :
> >
> > http://localhost:8080>
> > Order deny,allow
> > Allow from all
> >
> > RewriteEngine on
> >
> > # Define the authentication method
> > AuthType Basic
> > AuthName Galaxy
> > AuthUserFile /home/nate/htpasswd
> > Require valid-user
> > # Take the $REMOTE_USER environment variable and set it as a header
> in
> > the proxy request.
> > RewriteCond %{IS_SUBREQ} ^false$
> > RewriteCond %{LA-U:REMOTE_USER} (.+)
> > RewriteRule . - [E=RU:%1]
> > RequestHeader set REMOTE_USER %{RU}e
> >
> > RewriteRule ^/static/style/(.*)
> > /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
> > RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
> > RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
> > RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
> > RewriteRule ^(.*) http://localhost:8080$1 [P]
> >
> >
> >
> >
> > But several problems appeared when I launched my Galaxy.
> >
> >
> > First, must this instructions block be in the file apache2.conf or in the
> > file default of sites-available directory ?
> > If it must be in the file default, is it between the tags
> or
> > out of these tags ?
> >
> > Second, I've created an htpaswd file in my home directory, but when I
> launch
> > galaxy, it doesn't request me a login and password but it says me that
> > Galaxy requires an user authentification and it must be an error in my
> > apache configuration.
> > Is it a problem with the instructions or with their place in
> configuration
> > file ?
> >
> > Third the line appears two times in your instructions but
> it's
> > wrong for apache. I've deleted the first but I'm note sure that Rewrite
> > instructions must be in the block.
> >
> > And finally, I want to work with severals web processes and I want to add
> > this conf
[galaxy-dev] How must I configure Apache ?
Hi,
First, Sorry but, I'm a newbie with Apache and my questions will certainly
appear stupid.
To configure apache2, I've followed this wiki :
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
And I write these instructions :
http://localhost:8080> Order deny,allow Allow from all
RewriteEngine on # Define the
authentication method AuthType Basic AuthName Galaxy
AuthUserFile /home/nate/htpasswd Require valid-user # Take the
$REMOTE_USER environment variable and set it as a header in the proxy
request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond
%{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e RewriteRule
^/static/style/(.*)
/home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
^/static/(.*) /home/nate/galaxy-dist/static/$1 [L] RewriteRule
^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
But several problems appeared when I launched my Galaxy.
First, must this instructions block be in the file apache2.conf or in the
file default of sites-available directory ?
If it must be in the file default, is it between the tags or
out of these tags ?
Second, I've created an htpaswd file in my home directory, but when I
launch galaxy, it doesn't request me a login and password but it says me
that Galaxy requires an user authentification and it must be an error in my
apache configuration.
Is it a problem with the instructions or with their place in configuration
file ?
Third the line appears two times in your instructions but it's
wrong for apache. I've deleted the first but I'm note sure that Rewrite
instructions must be in the block.
And finally, I want to work with severals web processes and I want to add
this configuration lines :
...
Must I add to previous lines and where ? or Must I replace certain lines of
previous block and if yes : which lines ?
Thank you very much.
Julie
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Value error when running run.sh
Thanks It was the value of database_connection that was false ! I've changed it by : database_connection=mysql://cistrome:cistrome@localhost :8080/cistromeap?socket=/var/run/mysqld/mysqld.sock It works 2012/5/16 Nate Coraor > On May 16, 2012, at 5:15 AM, julie dubois wrote: > > > Hi, > > I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL > > I've configured apache 2 with this lines on file > /etc/apache2/sites-available/default between and > : > > > > http://localhost:8080";> > > > > Order Deny,Allow > > Allow from all > > > > RewriteEngine on > > RewriteRule ^/galaxy$ /galaxy/ [R] > > RewriteRule ^/galaxy/static/style/(.*) > /home/chevalier/galaxy-dist/static/june_2007_style/blue/$1 [L] > > RewriteRule ^/galaxy/static/scripts/(.*) > /home/chevalier/galaxy-dist/static/scripts/packed/$1 [L] > > RewriteRule ^/galaxy/static/(.*) /home/chevalier/galaxy-dist/static/$1 > [L] > > RewriteRule ^/galaxy/favicon.ico > /home/chevalier/galaxy-dist/static/favicon.ico [L] > > RewriteRule ^/galaxy/robots.txt > /home/chevalier/galaxy-dist/static/robots.txt [L] > > RewriteRule ^/galaxy/(.*) http://localhost:8080$1 [P] > > > > > > I've configured my MYSQL with a user who have all privilegies on a > database and in the universe_wsgi.ini the connection database appears like > this : > > > > database_connection = mysql://cistrome:cistrome@localhost > :/var/run/mysqld/mysqld.sock/cistromeap > > > > > > After running sh run.sh in my galaxy directory, I obtain this error > message : > > > > File > "/home/chevalier/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", > line 49, in __init__ > > self.port = int(port) > > ValueError: invalid literal for int() with base 10: ' ' > > > > This is the case too when I run this with root privilegies. > > Is it an error in my configuration of apache 2 or in MySQL ? Or is it an > error in my universe_wgsi.ini ? > > Hi Julie, > > It looks like the 'port =' option in universe.wsgi.ini is uncommented and > set to a blank value. Try setting it to 8080 (or comment it back out since > 8080 is the default). > > --nate > > > > > Thank you > > > > Julie > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Value error when running run.sh
Hi, I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL I've configured apache 2 with this lines on file /etc/apache2/sites-available/default between and : http://localhost:8080";> Order Deny,Allow Allow from all RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/chevalier/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/chevalier/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/chevalier/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/chevalier/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/chevalier/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy/(.*) http://localhost:8080$1 [P] I've configured my MYSQL with a user who have all privilegies on a database and in the universe_wsgi.ini the connection database appears like this : database_connection = mysql://cistrome:cistrome@localhost :/var/run/mysqld/mysqld.sock/cistromeap After running sh run.sh in my galaxy directory, I obtain this error message : File "/home/chevalier/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 49, in __init__ self.port = int(port) ValueError: invalid literal for int() with base 10: ' ' This is the case too when I run this with root privilegies. Is it an error in my configuration of apache 2 or in MySQL ? Or is it an error in my universe_wgsi.ini ? Thank you Julie ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
