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  • Jun 17 22:29
    AmandaBirmingham commented #3115
  • Jun 17 22:15
    antgonza commented #3115
  • Jun 17 22:11
    AmandaBirmingham commented #3115
  • Jun 17 20:07
    coveralls commented #3115
  • Jun 17 19:42
    AmandaBirmingham opened #3115
  • Jun 14 19:45
    antgonza commented #3114
  • Jun 14 19:44
    antgonza milestoned #3113
  • Jun 14 19:39
    FranckLejzerowicz closed #3114
  • Jun 14 19:39
    FranckLejzerowicz opened #3114
  • Jun 14 19:38
    wasade opened #3113
  • Jun 04 18:36
    antgonza commented #3054
  • Jun 04 18:24
    coveralls commented #3112
  • Jun 04 18:00
    antgonza synchronize #3112
  • Jun 04 16:42
    coveralls commented #3112
  • Jun 04 16:11
    antgonza opened #3112
  • Jun 04 16:11
    antgonza review_requested #3112
  • Jun 03 20:13
    mestaki commented #3054
  • Jun 02 18:32

    adswafford on dev

    fix #3095 Merge pull request #3109 from a… (compare)

  • Jun 02 18:32
    adswafford closed #3109
  • May 28 18:55

    wasade on dev

    fix #3101 fix errors deleting problematic study and 4 more (compare)

Jose Navas
@josenavas
One of the potential arguments to use qiita, is that we actually have to call the function purge_filepaths
adamrp
@adamrp
that's true, although if we exposed a CLI for purging filepaths, that would also work. I guess I just feel like 1) automatic management of users' files can be dangerous, 2) is not something everyone wants, and 3) shouldn't be managed by the web server
Jose Navas
@josenavas
I see your points, specially if qiita is installed in a single user mode
probably is something that we can include in the config file
Yoshiki Vázquez Baeza
@ElDeveloper
Sorry to jump in this a bit late, but I like more the idea of providing a CLI that enables this in an easy way
Yoshiki Vázquez Baeza
@ElDeveloper
So, we are ready to merge the cart-branch into master?
Jose Navas
@josenavas
I don’t think so
I just did a follow up on the latest merged PR from @squirrelo
@antgonza identified that is something that needs improvement, and I agree with him, so a solution is needed
Joshua Shorenstein
@squirrelo
We don't need it now since it is 100% functional and it's alpha 0.1 Please just open an issue since this is a tiny detail holding up the entire project
Jose Navas
@josenavas
it’s not holding anything
I can continue working
Jose Navas
@josenavas
hey guys, can I have biocore/qiita#1073 reviewed?
Yoshiki Vázquez Baeza
@ElDeveloper
hey cheetahs, I was going to start reviewing, first with #1275 and with #1276
just wanted to make sure this is what I should be doing
*the order in which I should be doing this
Joshua Shorenstein
@squirrelo
They are independent so should be fine
Jose Navas
@josenavas
you can do #1275 and #1276 independently. However, before doing #1275 I think #1256 should be reviewed
I’m reviewing right now #1256
Yoshiki Vázquez Baeza
@ElDeveloper
It seems like @antgonza and you were already on top of #1256 so, I'll let you guys finish with it :sparkles:
Jose Navas
@josenavas
ok!
Yoshiki Vázquez Baeza
@ElDeveloper
thanks!
Yoshiki Vázquez Baeza
@ElDeveloper
Just in case someone is interested, this is how the document looks rendered: http://nipy.bic.berkeley.edu:5000/download/14
Greg Caporaso
@gregcaporaso
hey, is it possible to download the sff file for the keyboard study from qiita directly? fierer_forensic_keyboard
Yoshiki Vázquez Baeza
@ElDeveloper
@gregcaporaso No, we do not provide a way to retrieve the raw data
Jose Navas
@josenavas
Hey guys if somebody is available we have a problem with the live system any kind of support will be appreciated
Greg Caporaso
@gregcaporaso
hi all, what’s the official qiita URL? I want to reference it in a paper I’m working on
Yoshiki Vázquez Baeza
@ElDeveloper
that would be qiita.microbio.me
Greg Caporaso
@gregcaporaso
thanks
Yoshiki Vázquez Baeza
@ElDeveloper
NP
Cale Seymour
@BassMakesPaste
Is there a way to download every biom file on Qiita with associated metadata and package them together? I've been scouring the site for a week or so and can't find anything.
Antonio Gonzalez
@antgonza
Not at the moment as you need to do it one by one. Note that we are working on RESTful interface to make this easier but this is still on the works.
Greg Caporaso
@gregcaporaso
hey qiita-ers, what’s the file type of a “preprocessed demux” file? and what is in this file? I’m trying to share data from a study with someone, and i want to give them the mapping file and post split libraries sequences.
Jose Navas
@josenavas
hey @gregcaporaso
the preprocessed demux file is an hdf5 file that contains the demultiplexed sequences in a per-sample basis. It is an alternative representation of a FASTQ which allows faster per sample access
Prior discussions with @wasade lead to also an alternative implementation of the OTU map using hdf5 that is going to work in conjunction with this implementation of the demux file. I still didn’t had time to code it, but I’m planning to do so during the following 2 weeks.
Greg Caporaso
@gregcaporaso
ok, thanks for the reply
i chatted with @antgonza about it this morning too. my recommendation is that what these files are is better documented - i was looking for demultiplexed sequence data (in fna.gz format) and that was the one i thought i wanted. i couldn’t open it with gunzip or unzip, but could tell that it was binary, so was pretty confused. he mentioned that you guys are re-doing that page, so sounds like the better documentation of this stuff is already in progress
Greg Caporaso
@gregcaporaso
qiita devs: i know i’ve asked this before, but the preferred url is qitta.ucsd.edu?
Jose Navas
@josenavas
Nope, the preferred url is qiita.microbio.me
Greg Caporaso
@gregcaporaso
thanks!
Jose Navas
@josenavas
Sure!
Bradley Stevenson
@bsteve1120
qiita devs, I would like to include some stats to a proposal (in which I plan on using qiita) that describe the growth in size of this database over the last year(s). Can anyone point me in that direction or throw some stats at me?
Antonio Gonzalez
@antgonza
Hi @bsteve1120, we currently don't have something like this but we think is a good idea. However, we need to discuss internally what will be the best info to have available. Anyway, I'm wondering if you have a deadline for this?
Bradley Stevenson
@bsteve1120
@antgonza, thanks for considering this. The proposal is due Feb 5th so if i had the information by the 3rd, it will likely make it in. I will be pitching this to an audience who might not be familiar with Qiita and i would like to make the case that it reslly is the best resource for meta analyses of sequence data across many studies. Thanks for considering this!
Antonio Gonzalez
@antgonza
@bsteve1120, I have added an issue about this (biocore/qiita#1636) and you can find some basic stats here (retrieved on 012916): https://www.dropbox.com/s/sdbh9wlh9d1lc0d/qiita-file-stats-012916.txt?dl=0. Hope this helps.
Bradley Stevenson
@bsteve1120
Thank you @antgonza! Are these values the total for each time period/month? I ask because the numbers fluctuate and I expected them to be cumulative. Not to worry, I can do the math, I just wanted to confirm. Thanks again!
Antonio Gonzalez
@antgonza
@bsteve1120 yes total for each month => you need to add them.