Re: [galaxy-dev] Doubts about FTP upload.

[Jennifer Hillman-Jackson]

Hello,

The server name is *usegalaxy.org * (no ftp://
prefix).

Full FTP upload help is here: https://galaxyproject.org/ftp-upload/

Thanks!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Apr 11, 2018 at 12:20 PM, Álvaro Rios 
wrote:

> Dear
>
> I am trying to upload files via FTP. However, the following message
> appears.
>
> "Authentication required ftp://usegalaxy.org Your connection to this site
> is not private." I do not have the experience to use galaxy, What I need to
> do?
>
> Thank you.
>
> Álvaro Rios.
>
>
>
>
> ___
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>
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[galaxy-dev] Doubts about FTP upload.

[Álvaro Rios]

Dear

I am trying to upload files via FTP. However, the following message appears.

"Authentication required ftp://usegalaxy.org Your connection to this site
is not private." I do not have the experience to use galaxy, What I need to
do?

Thank you.

Álvaro Rios.
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Re: [galaxy-dev] fonts on headless compute nodes

[Björn Grüning]

Hi Matthias,

can you make sure FASTQC gets the openjdk version from conda-forge and 
not from defaults? This will fix our one problem.


MetaProSIP should add additional dependencies to the conda package. 
Ideally no requirements are needed on the system level. This is not 
always possible, for example for opengl dependent stuff, but we should 
try to fix the conda package as much as possible as this will give us 
also robust containers.


Cheers,
Bjoern

Am 11.04.2018 um 14:51 schrieb Matthias Bernt:

Dear list,

I found that some tools (eg FastQC and MetaProSIP) have problems with 
missing fonts (the former is java and the latter caused by R) on our 
compute nodes which do not have xorg and no fonts installed.


On the cluster head nodes several font related packages are installed:

dejavu-fonts-common-2.33-1.el6.noarch
xorg-x11-fonts-Type1-7.2-11.el6.noarch
liberation-fonts-common-1.05.1.20090721-5.el6.noarch
liberation-sans-fonts-1.05.1.20090721-5.el6.noarch
dejavu-sans-fonts-2.33-1.el6.noarch
urw-fonts-2.4-11.el6.noarch
ghostscript-fonts-5.50-23.2.el6.noarch
xorg-x11-fonts-misc-7.2-11.el6.noarch

It seems that conda no fonts are available. Is there somebody with 
similar problems. Any hint which of the packages is/are actually needed. 
Maybe our admins could install them...


I also found for MetaProSIP that several xorg-... packages are needed. 
Should such dependencies be handled by the conda packages or by the 
Galaxy tool.


Best,
Matthias





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[galaxy-dev] April Galactic News: UseGalaxy.org gets some siblings, GCCBOSC and other event news; new pubs, servers, jobs, ...

[Dave Clements]

Hello all,

The April 2018 Galactic News
 highlights what's going
on in the Galaxy (and it's actually quite cool). Take a look:

   - *UseGalaxy.eu and UseGalaxy.org.au Launched
   
*
   - Lots of GCCBOSC 2018 news
   :
  - We are pleased to announce that Lucia Peixoto
   of
  Washington State University will be our third keynote speaker.
  - Please welcome *Google Cloud
  * as
  a GCCBOSC Platinum sponsor.
  - *GCC Lightning talk, poster and demo submissions are due by April
  16
  
*
  - Childcare for GCCBOSC
  !
  Space is limited, so register *now*.
   - Upcoming Events:
  - 2018 Big Genomics Data Skills Training course
  

   - how to integrate genomic data analysis into undergraduate
  coursework
  - Gateways 2018 Call for Participation
  

  - Upcoming events
   (on
  four continents)
   - New:
  - 119 publications
  
(including
  9 highlighted ones)
  - Openings in 9 groups on 2 continents
  
  - Public Galaxy Server News
  

   (a new server and an updated one too)
  - ToolShed contributions
  
  - Releases
   of
  Galaxy, Galaxy Docker, blend4j, and galaxy-lib
   - And other news
    too

See the newsletter  for
the full story, and we hope to see you in Portland!
Dave C, on behalf of the Galaxy

-- 
https://gccbosc2018.sched.com/
https://galaxyproject.org/
https://usegalaxy.org/
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[galaxy-dev] fonts on headless compute nodes

[Matthias Bernt]

Dear list,

I found that some tools (eg FastQC and MetaProSIP) have problems with 
missing fonts (the former is java and the latter caused by R) on our 
compute nodes which do not have xorg and no fonts installed.


On the cluster head nodes several font related packages are installed:

dejavu-fonts-common-2.33-1.el6.noarch
xorg-x11-fonts-Type1-7.2-11.el6.noarch
liberation-fonts-common-1.05.1.20090721-5.el6.noarch
liberation-sans-fonts-1.05.1.20090721-5.el6.noarch
dejavu-sans-fonts-2.33-1.el6.noarch
urw-fonts-2.4-11.el6.noarch
ghostscript-fonts-5.50-23.2.el6.noarch
xorg-x11-fonts-misc-7.2-11.el6.noarch

It seems that conda no fonts are available. Is there somebody with 
similar problems. Any hint which of the packages is/are actually needed. 
Maybe our admins could install them...


I also found for MetaProSIP that several xorg-... packages are needed. 
Should such dependencies be handled by the conda packages or by the 
Galaxy tool.


Best,
Matthias




--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

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Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

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Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
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