gatoravi

gatoravi

List lsf job groups bjgroup -s /username

Make a new one: bgadd -L <job_limit> <name>

Alter the limit later: bgmod

gatoravi

df $path and df -i $path to check space and inodes

gatoravi

rm -f simulated_hets.bam && python simulate_bam_reads.py  ~/dat/ref/hs37d5/all_sequences.fa 0.5 1:100000 1:100200 1:10040       0 1:100600 1:100800 | samtools view  -bh > simulated_hets.bam && samtools index simulated_hets.bam
rm -f simulated_hets.bam && python simulate_bam_reads.py  ~/dat/ref/hs37d5/all_sequences.fa 1.0 1:100000 1:100200 1:10040       0 1:100600 1:100800 | samtools view  -bh > simulated_homs.bam && samtools index simulated_homs.bam
rm -f cis_ase_tumor_rna.bam && python simulate_bam_reads.py  ~/src/regtools/tests/integration-test/data/fa/test_chr22.fa        0 22:1050 22:1550 22:1950 22:2050 22:2550 22:2950 22:3050 22:3550 22:3950 | samtools view  -bh > cis_ase_tumor_rna.bam && samtools index cis_ase_tumor_rna.bam
rm -f cis_ase_tumor_dna.bam && python simulate_bam_reads.py  ~/src/regtools/tests/integration-test/data/fa/test_chr22.fa        0.5 22:1050 22:1550 22:1950 22:2050 22:2550 22:2950 22:3050 22:3550 22:3950 | samtools view  -bh > cis_ase_tumor_dna.bam && samtools index cis_ase_tumor_dn

gatoravi

• Intelligent investor, genuinely serious book on investing and how to read markets...but like a textbook
• Short history of nearly everything by Bill Bryson, must read - damn cool book
• Good to Great...amazing book if u want to learn how to study companies...seemingly easy to read but can make it tough for yourself if u want to get into nitty gritty...
• Buffett by Roger Lowenstein
• Barbarians at the Gate, for fiction feel of a non fiction story...good time pass...
• Rise and Fall of Nations by Ruchir sharma
• Fooled by randomness, book about stats and how markets are

gatoravi

• Aaranya kaandam
• Madras
• Thani oruvan
• Joker (2016)
• Pariyerum Perumal BA.BL
• Andhadhun
• Ittefaq
• Evaru (same as Badla)

gatoravi

sacct -u aru
      JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
5718685      interacti+ interacti+      dcl          1  COMPLETED      0:0
5718686      interacti+ interacti+      dcl          1  COMPLETED      0:0

sacct -j 5719109 --format=JobID,JobName,MaxRSS,Elapsed
JobID JobName MaxRSS Elapsed

gatoravi

The default soft (warning) and hard (error) size limits are set to 500,000 and 10,000,000 bytes but can be overriden through the hooks.filesizesoftlimit and hooks.filesizehardlimit settings respectively:

$ git config hooks.filesizesoftlimit 100000
$ git config hooks.filesizehardlimit 4000000

gatoravi

> counts <- rnbinom(1000, size = 10, p = 0.1)
> mu <- mean(counts)
> p <- mu/var(counts)
> r <- mu ^ 2/(var(counts) - mu)
> hist(counts, freq = F)
> curve(dnbinom(x, size = r, prob = p), from = 0, to = max(counts), n = max(counts) + 1)

gatoravi

first_time <- function() {
    t1 <- read.table("../ALL.chrY.phase3_integrated_v1b.20130502.genotypes.vcf.gz")
    print(nrow(t1))
    nucs <- c('A', 'C', 'G', 'T')
    t1 <- t1[t1$V4 %in% nucs & t1$V5 %in% nucs, ]
    print(nrow(t1))
    t2 <- t1[, 10:ncol(t1)]
    t2 <- sapply(t2, as.character)
    save(t2, file = "t2")
}