User: spollack

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spollack0
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Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston
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s*******@jimmy.harvard.edu

Posts by spollack

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Problem with IRanges and GenomicRanges
... Aha, now I get it. These aren't points on the real line; they're segments.  |--1--|--2--|--3--|--4--|--5--|--6--| So |--2--|--3--| is adjacent to |--4--|--5--|   ...
written 4 weeks ago by spollack0
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Comment: C: Problem with IRanges and GenomicRanges
... Confused. How can the distance between [4,5] and [2,3] be zero? The documentation for nearest-methods {IRanges} says: x and y overlap => distance(x, y) == 0 or x and y overlap or are adjacent <=> distance(x, y) == 0  [4,5] and [2,3] do not overlap and they are not adjacent. Wh ...
written 4 weeks ago by spollack0
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Problem with IRanges and GenomicRanges
... Dear Bioconductor, I think it is possible that recent modifications to IRanges and GenomicRanges broke our bumphunter package. bumphunter does a very simple test that amounts to this: R> x <- data.frame(start = c(2, 4, 7, 10, 13, 17, 19, 22, 24), end = c(3, 5, 9, 12, 16, 18, 20, 23, 26), c ...
iranges genomicranges written 5 weeks ago by spollack0 • updated 5 weeks ago by Hervé Pagès ♦♦ 12k
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Comment: C: Using AMI with StarCluster - error authenticating
... OK, thanks, good idea (Bioconductor Docker), I'll try that.  - S ...
written 7 months ago by spollack0
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Comment: C: Using AMI with StarCluster - error authenticating
... Thanks for the advice. I tried to build a cluster with CfnCluster and the Bioconductor AMI but I never did get it to work. My best attempt was a config file with this: master_instance_type = t2.large slave_instance_type = t2.large master_root_volume_size = 500 slave_root_volume_size = 500 base_os = ...
written 7 months ago by spollack0
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Comment: C: Using AMI with StarCluster - error authenticating
... Sorry, just saw this. I got the AMI to work with the latest StarCluster version 0.95.6 yesterday. But now I have a problem with connecting to Rstudio Server. I can connect to rstudio server on a slave node just fine, but I can't connect to it on the master node. On the master node, I get the login ...
written 7 months ago by spollack0
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Using AMI with StarCluster - error authenticating
... Dear Bioconductor, I am attempting to follow the instructions here https://www.bioconductor.org/help/bioconductor-cloud-ami/#configuring_starcluster to configure a StarCluster for running the Bioconductor AMI as a cluster. But I am getting an error when I try to start a cluster. The error is a Pyt ...
ami written 8 months ago by spollack0 • updated 8 months ago by Dan Tenenbaum ♦♦ 8.1k

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