On Jul 17, 2015 11:00 AM, <galaxy-dev-requ...@lists.galaxyproject.org>
wrote:

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> Today's Topics:
>
>    1. Re: yaml import problem on startup (Marius van den Beek)
>    2. Re: yaml import problem on startup (Marius van den Beek)
>    3. Re: yaml import problem on startup (Poole, Richard)
>    4. Re: Data Libraries: Unable to Link to Files When Paths
>       Contain Spaces (John Chilton)
>    5. Re: Error sorting or uploading Bam File (John Chilton)
>    6. Re: CloudMan auto-scaling - Use spot instance for worker
>       node? (Alexander Vowinkel)
>    7. Re: Download data by data manager with non generic        ftp-proxy
>       (John Chilton)
>    8. Re: CloudMan auto-scaling - Use spot instance for worker
>       node? (Enis Afgan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 17 Jul 2015 12:23:06 +0200
> From: Marius van den Beek <m.vandenb...@gmail.com>
> To: "Poole, Richard" <r.po...@ucl.ac.uk>
> Cc: "galaxy-dev@lists.galaxyproject.org"
>         <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] yaml import problem on startup
> Message-ID:
>         <
> cacjqqiqo3uti7-dovvg_1l7-rzkwsxh9ccz2nsfjfurg+kg...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Richard,
>
> Well, I do have the same problem now (running bamtools), after applying the
> patch that should fix
> metadata issue we discussed yesterday.
> I'll dig into this.
>
> Marius
>
> On 17 July 2015 at 11:37, Poole, Richard <r.po...@ucl.ac.uk> wrote:
>
> >  Hi all,
> >
> >  With the most recent update of Galaxy and also OS X 10.10.4 I am seeing
> > this error message when first starting up the server:
> >
> >   /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning:
> > Module yaml was already imported from
> >
> /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc,
> > but
> >
> /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg
> > is being added to sys.path
> >    self.check_version_conflict()
> >
> >  This then is preventing certain tools from running correctly (such as
> > samtools_filter (jjohnson) and they give the same error message when they
> > fail:
> >
> >  /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning:
> Module yaml was already imported from
> /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc,
> but
> /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg
> is being added to sys.path
> >   self.check_version_conflict()
> >
> > Any thoughts?
> >
> >  Thanks,
> > Richard
> >
> > *Richard J Poole PhD*
> >  Wellcome Trust Fellow
> > Department of Cell and Developmental Biology
> > University College London
> > 21 University Street, London WC1E 6DE
> > Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
> > Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)
> >
> >
> > ___________________________________________________________
> > 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:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
> >
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> ------------------------------
>
> Message: 2
> Date: Fri, 17 Jul 2015 13:00:24 +0200
> From: Marius van den Beek <m.vandenb...@gmail.com>
> To: "Poole, Richard" <r.po...@ucl.ac.uk>
> Cc: "galaxy-dev@lists.galaxyproject.org"
>         <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] yaml import problem on startup
> Message-ID:
>         <
> cacjqqiqh9f2410hc6h-r+5rcnhsdviwzkg1m+ungyk-mdda...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Richard,
>
> Reverting the patch allows normal finishing of jobs, so unfortunately it
> seems
> we get a double import somewhere in the patch ... i'm suspecting it's
>
> *from* galaxy *import* app
>
> in lib/galaxy/model/custom_types.py, but I don't know how to circumvent
> this.
>
> Marius
>
>
> On 17 July 2015 at 12:23, Marius van den Beek <m.vandenb...@gmail.com>
> wrote:
>
> > Hi Richard,
> >
> > Well, I do have the same problem now (running bamtools), after applying
> > the patch that should fix
> > metadata issue we discussed yesterday.
> > I'll dig into this.
> >
> > Marius
> >
> > On 17 July 2015 at 11:37, Poole, Richard <r.po...@ucl.ac.uk> wrote:
> >
> >>  Hi all,
> >>
> >>  With the most recent update of Galaxy and also OS X 10.10.4 I am seeing
> >> this error message when first starting up the server:
> >>
> >>   /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning:
> >> Module yaml was already imported from
> >>
> /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc,
> >> but
> >>
> /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg
> >> is being added to sys.path
> >>    self.check_version_conflict()
> >>
> >>  This then is preventing certain tools from running correctly (such as
> >> samtools_filter (jjohnson) and they give the same error message when
> they
> >> fail:
> >>
> >>  /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning:
> Module yaml was already imported from
> /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc,
> but
> /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg
> is being added to sys.path
> >>   self.check_version_conflict()
> >>
> >> Any thoughts?
> >>
> >>  Thanks,
> >> Richard
> >>
> >> *Richard J Poole PhD*
> >>  Wellcome Trust Fellow
> >> Department of Cell and Developmental Biology
> >> University College London
> >> 21 University Street, London WC1E 6DE
> >> Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
> >> Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)
> >>
> >>
> >> ___________________________________________________________
> >> 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:
> >>   https://lists.galaxyproject.org/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>   http://galaxyproject.org/search/mailinglists/
> >>
> >
> >
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> ------------------------------
>
> Message: 3
> Date: Fri, 17 Jul 2015 12:05:20 +0000
> From: "Poole, Richard" <r.po...@ucl.ac.uk>
> To: Marius van den Beek <m.vandenb...@gmail.com>
> Cc: "galaxy-dev@lists.galaxyproject.org"
>         <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] yaml import problem on startup
> Message-ID: <d6388e22-7088-4e9b-85a5-6ec26350d...@live.ucl.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Marius,
>
> I can also confirm that switching branches to revert the patch allows
> normal finishing of jobs. So its clearly related to the patches we applied
> yesterday to fix the metadata issue (see [galaxy-dev] Slow responses
> viewing histories).
>
> However, I have noticed that even on an older non-patched branch of 15.05
> I am still getting the same UserWarning about double yaml import upon
> Galaxy startup. So perhaps something about the metadata patches is somehow
> turning this warning into a tool fail?
>
> Rich
>
> On 17 Jul 2015, at 12:00, Marius van den Beek <m.vandenb...@gmail.com
> <mailto:m.vandenb...@gmail.com>> wrote:
>
> Hi Richard,
>
> Reverting the patch allows normal finishing of jobs, so unfortunately it
> seems
> we get a double import somewhere in the patch ... i'm suspecting it's
>
> from galaxy import app
>
> in lib/galaxy/model/custom_types.py, but I don't know how to circumvent
> this.
>
> Marius
>
>
> On 17 July 2015 at 12:23, Marius van den Beek <m.vandenb...@gmail.com
> <mailto:m.vandenb...@gmail.com>> wrote:
> Hi Richard,
>
> Well, I do have the same problem now (running bamtools), after applying
> the patch that should fix
> metadata issue we discussed yesterday.
> I'll dig into this.
>
> Marius
>
> On 17 July 2015 at 11:37, Poole, Richard <r.po...@ucl.ac.uk<mailto:
> r.po...@ucl.ac.uk>> wrote:
> Hi all,
>
> With the most recent update of Galaxy and also OS X 10.10.4 I am seeing
> this error message when first starting up the server:
>
> /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module
> yaml was already imported from
> /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc,
> but
> /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg
> is being added to sys.path
>   self.check_version_conflict()
>
> This then is preventing certain tools from running correctly (such as
> samtools_filter (jjohnson) and they give the same error message when they
> fail:
>
>
> /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module
> yaml was already imported from
> /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc,
> but
> /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg
> is being added to sys.path
>   self.check_version_conflict()
>
> Any thoughts?
>
> Thanks,
> Richard
>
> Richard J Poole PhD
> Wellcome Trust Fellow
> Department of Cell and Developmental Biology
> University College London
> 21 University Street, London WC1E 6DE
> Office (518 Rockefeller): +44 20 7679
> 6577<tel:%2B44%C2%A020%207679%206577> (int. 46577)
> Lab (529 Rockefeller): +44 20 7679 6133<tel:%2B44%2020%C2%A07679%206133>
> (int. 46133)
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
>
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> ------------------------------
>
> Message: 4
> Date: Fri, 17 Jul 2015 15:52:22 +0100
> From: John Chilton <jmchil...@gmail.com>
> To: Joseph Brent Greer <joseph.gr...@northwestern.edu>
> Cc: "galaxy-dev@lists.galaxyproject.org"
>         <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] Data Libraries: Unable to Link to Files When
>         Paths Contain Spaces
> Message-ID:
>         <
> canwbokd0jcb_ncvzpm9tbxpjhci+8x8dam8hk5wddjze2wz...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> This is a good news, bad news sort of thing. I have opened a PR to fix
> the actual uploads here -
> https://github.com/galaxyproject/galaxy/pull/474. But I think many
> tools don't properly quote file paths with names in them - so I
> suspect you will find a lot of tool bugs using these files.
>
> Thanks for the bug report.
>
> -John
>
>
> On Mon, Jul 6, 2015 at 10:11 PM, Joseph Brent Greer
> <joseph.gr...@northwestern.edu> wrote:
> >
> >
> > Hi All,
> >
> >
> >
> > We’re having problems adding files to data libraries.
> >
> >
> >
> > We’d like to create links to files instead of copying them into Galaxy.
> We
> > can create links if there aren’t spaces in the paths. Also, we can copy
> > files into libraries even if there are spaces in the paths.
> >
> >
> >
> > Unfortunately, we cannot create links to files when their paths contain
> > spaces.
> >
> >
> >
> > The job standard error and miscellaneous information are:
> >
> >
> >
> > Miscellaneous information:uploaded RAW file Traceback (most recent call
> > last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py",
> line 1,
> > in <module> from galaxy_ext.metadata.set_metadata import set_metadata;
> > set_metadata() File "/home/galaxy/Galaxy/galaxy-dist
> >
> > Job Standard Error
> >
> > Traceback (most recent call last):
> >
> >   File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1,
> in
> > <module>
> >
> >     from galaxy_ext.metadata.set_metadata import set_metadata;
> > set_metadata()
> >
> >   File
> >
> "/home/galaxy/Galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py",
> > line 80, in set_metadata
> >
> >     filename_out = fields.pop( 0 )
> >
> > IndexError: pop from empty list
> >
> > error
> >
> >
> >
> > We’ve set allow_library_path_paste = True in galaxy.ini.
> >
> >
> >
> > We’ve also tried adding “” or ‘’ around the path and get the following
> error
> > message:
> >
> >
> >
> > Invalid paths: “home/galaxy/Galaxy/galaxy-dist/”/share/projects/2014
> Test””
> >
> >
> >
> > Any help or suggestions would be great.
> >
> >
> >
> > Thanks,
> >
> >
> >
> > Joe Greer
> >
> > Proteomics Center of Excellence
> >
> > Northwestern University
> >
> >
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________
> > 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:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 17 Jul 2015 16:08:19 +0100
> From: John Chilton <jmchil...@gmail.com>
> To: julie dubois <dubju...@gmail.com>
> Cc: "galaxy-...@lists.bx.psu.edu" <galaxy-...@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] Error sorting or uploading Bam File
> Message-ID:
>         <
> canwbokelsgb0uqpxn3kxwpvxlzkijinbwmnvacbjwskohr8...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I'm not the right person to respond to this but since no one else has
> I will explain my limited (probably incorrect) understanding of the
> problem and what needs to be done. I believe Galaxy assumes all bam
> files are coordinated sorted by default - so Galaxy's bam datatype
> would be better thought of as a coordinate-sorted bam. Certain people
> do not want to allow non-coordinate sorted bam files because these
> would be allowed by Galaxy as valid as inputs to tools that expect
> sorted bams - and things would break. For the same reason I imagine
> these people would argue the bai file needs to be generated because
> certain tools will depend on its existence.
>
> I believe the proposed solution is to add an unsorted bam datatype to
> Galaxy. I don't know if there is any work in progress on this but it
> seems to be needed by many researchers.
>
> Hope this clarifies things somewhat,
> -John
>
>
> On Mon, Jun 29, 2015 at 11:06 AM, julie dubois <dubju...@gmail.com> wrote:
> > Hi all,
> >
> > My galaxy is the last update and I work with samtools 1.2.
> > I have a bug with the sorting and the upload of bam file.
> > This bug appears only when I try to upload bam sorted by name or when
> > I try to sort by name.
> > When I work with bam sorted by coordinate, there is no problem.
> >
> > So, when I try to sort a bam file by name, this error appears under
> > the "bug icon" :
> >
> > Tool execution generated the following error message:
> > [bam_sort_core] merging from 20 files...
> > *** Error in `python': double free or corruption (!prev):
> 0x0000000002897990 ***
> > Aborted (core dumped)
> >
> > The tool produced the following additional output:
> >
> > [E::hts_idx_push] chromosome blocks not continuous
> > Galaxy attempted to build the BAM index with samtools 1.0+ but failed:
> > [Errno 2] No such file or directory:
> >
> '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai'
> >
> > And the same type of error appears when I try to upload bam sorted by
> name.
> >
> >
> > What I understand is that the bam can be sorted properly (The command
> > line to sort is ok in a terminal with no bug and I can follow this
> > step in the job_working_directory during the run) but Galaxy seems to
> > fail to create a bai.
> >
> > For our analysis pipeline, I think the bai is not crucial, is it
> > possible to avoid this creation of bai during uploading and sorting of
> > bam file by name ?
> >
> > Is there another problem than this creation of bai ?
> >
> > 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:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 17 Jul 2015 10:27:29 -0500
> From: Alexander Vowinkel <vowinkel.alexan...@gmail.com>
> To: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] CloudMan auto-scaling - Use spot instance
>         for     worker node?
> Message-ID:
>         <CANPh1r_Hvb=M1J=
> xkw5pua-_a0cyocy9cka_o1nhgiqm4rm...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> I am referring to this:
>
> http://dev.list.galaxyproject.org/CloudMan-auto-scaling-Use-spot-instance-for-worker-node-tp4665813p4665835.html
>
> I would give an upvote for spot instances for auto-scaling.
>
> Have there been more ideas about this since?
>
> Best,
> Alexander
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> ------------------------------
>
> Message: 7
> Date: Fri, 17 Jul 2015 16:33:06 +0100
> From: John Chilton <jmchil...@gmail.com>
> To: Tobias Zimmermann
>         <tobias.zimmerm...@computational.bio.uni-giessen.de>
> Cc: "galaxy-dev@lists.galaxyproject.org"
>         <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] Download data by data manager with non
>         generic ftp-proxy
> Message-ID:
>         <
> canwbokevw1pydukfvvrt21zqduyhryytmcivhxmfqnh32xo...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Yeah - it seems like ftplib doesn't support proxies and that is what
> is used by this script:
>
>
> https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py
>
> Some relevant discussion here:
>
> http://stackoverflow.com/questions/1293518/proxies-in-python-ftp-application
>
> I might suggest reworking that script to use urllib2 which should
> support ftp and proxies. Not sure if there is some feature in ftplib
> though that is required for the data manager.
>
> -John
>
>
> On Mon, Jun 15, 2015 at 11:12 AM, Tobias Zimmermann
> <tobias.zimmerm...@computational.bio.uni-giessen.de> wrote:
> > Dear All,
> > I have some problems with the download of genome files by the data
> manager.
> > I tried to download some genome files from the UCSC server with the data
> > manager of galaxy ( name: data_manager_fetch_genome_all_fasta, revision:
> > cca219f2b212), but it fails because of a timeout. Our galaxy server is
> in an
> > internal network without connection to the Internet. To access the
> Internet
> > we are required to go trough a http-proxy before any web-services can be
> > accessed.
> >
> > The file
> > /shed_tools/
> toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py
> > manages the download of the file. Line 183 shows the problem. Here the
> FTP
> > item from the python ftplib module tries to establishes the connection to
> > the UCSC ftp server. This connection fails. So here is my question:
> >
> > How can i download data by the data manager with a http-proxy?
> >
> >
> > Regards
> > Tobias
> >
> > ___________________________________________________________
> > 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:
> >  https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >  http://galaxyproject.org/search/mailinglists/
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 17 Jul 2015 11:41:53 -0400
> From: Enis Afgan <enis.af...@irb.hr>
> To: Alexander Vowinkel <vowinkel.alexan...@gmail.com>
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] CloudMan auto-scaling - Use spot instance
>         for     worker node?
> Message-ID:
>         <
> cacj_meq4lo9nbjnynyrvq8jgkn0t-vppha2ywci0ytwrzl0...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I've created a trello card for this, hence making it adding it to the
> actual todo list: https://trello.com/c/cqEwunvl
> Not sure when I'll get to this but it'll get done.
>
> Thanks.
>
> On Fri, Jul 17, 2015 at 11:27 AM, Alexander Vowinkel <
> vowinkel.alexan...@gmail.com> wrote:
>
> > Hi,
> >
> > I am referring to this:
> >
> >
> http://dev.list.galaxyproject.org/CloudMan-auto-scaling-Use-spot-instance-for-worker-node-tp4665813p4665835.html
> >
> > I would give an upvote for spot instances for auto-scaling.
> >
> > Have there been more ideas about this since?
> >
> > Best,
> > Alexander
> >
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