[galaxy-user] upload problem

2012-06-14 Thread sujata dhar
Hello, I am trying to upload 27.2 GB fastq file in Galaxy through FTP, but it throws an error: netout: Connection reset by peer 421 Service not available,remote server has closed connection. Please help. Thank you, Sujata ___ The Galaxy

[galaxy-user] Reference genome , fasta with or without gene feature

2012-06-14 Thread Ateequr Rehman
Dear All I am analysing bacterial RNA seq (illumina). as my reference genome is not in galaxy. so i need to downlaoded the reference genome from  NCBI and upload to my history Should i use reference genome with  gene features or  single  fasta file with out any annotation information. even

Re: [galaxy-user] Galaxy Reference Genome

2012-06-14 Thread Loraine, Ann
This explanations is very clear. Thank you – I was wondering about some of these issues as well. It would be wonderful if Galaxy could somehow make it possible to provide a bed file for the –G option or make it feasible to use GTF/bed output from the Table Browser tool as input to the –G

[galaxy-user] Page edition bug

2012-06-14 Thread Felix Homa
Hi Galaxy team, I have two instances of galaxy on the same host, and have enabled page edition (I set enable_pages = True on universe_wsgi.ini file). I have set the parameter cookie_path different for each instance. I'm disconnected from galaxy when I try to edit a page content. But when I

[galaxy-user] FTP down?

2012-06-14 Thread John Clayton
Dear Sir or Madam, I have been attempting to upload a few datasets (2Gb) for the past few days but I cannot seem to login to the server. This has been the case since the server crashed last week. Could you please restart the ftp server? Many thanks, John -- John R. Clayton, PhD Université

[galaxy-user] FTP Error 530 Sorry, the maximum number of clients (3) for this user are already connected.

2012-06-14 Thread Christopher M. Weber
Hello, I have been unable to get a solid FTP connection to main.g2.bx.psu.edu for ~24hrs. Two things have occurred: 1) I get the error 530 Sorry, the maximum number of clients (3) for this user are already connected or 2) when finally connected, some files fail during transfer with

[galaxy-user] generate pileup not working?

2012-06-14 Thread Lilach Friedman
Hi, I am trying to do variants call with generate pileup. My steps where: 1. BWA 2. select only lines with the pattern Matching pattern: XT:A:U 3. SAM-to-BAM 4. then I tried to use Generate pileuphttps://main.g2.bx.psu.edu/tool_runner?tool_id=sam_pileupfrom BAM dataset However, it does not work,