Skip to content

Instantly share code, notes, and snippets.

View lindenb's full-sized avatar
😶
I hate people.

Pierre Lindenbaum lindenb

😶
I hate people.
525 followers · 80 following
View GitHub Profile
@lindenb
lindenb / tags.md
Last active May 11, 2024 20:45
instagram and redditgetsdrawn rgd
@lindenb
lindenb / Delicious2Diigo.java
Created December 19, 2010 14:48
Save bookmarks from delicious to Diigo.com using the Diigo API.
/**
* Delicious2Diigo
*
* Author:
* Pierre Lindenbaum
* http://plindenbaum.blogspot.com
*
* Motivation:
* save bookmarks from delicious to diigo using the Diigo API.
*
@lindenb
lindenb / bcftools-gvf.nf
Created May 23, 2019 10:11
calling bams in gvcf mode with bcftools nextflow
reference=file("${params.reference}")
bams=file("${params.bams}")
process getChromosomes {
tag "get chromosomes from ${ref}"
executor 'local'
input:
file ref from reference
output:
@lindenb
lindenb / biostar9592523.sparql
Last active April 12, 2024 19:04
https://www.biostars.org/p/9592523/ Can you suggest a protein that has two chainst but only 50 total number of atoms?
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX vg: <http://biohackathon.org/resource/vg#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
PREFIX uberon: <http://purl.obolibrary.org/obo/uo#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX sp: <http://spinrdf.org/sp#>
@lindenb
lindenb / Makefile
Created April 4, 2024 10:59
Tool to Identify Gene, Regulatory Role, and Function at Integration Sites https://www.biostars.org/p/9591769/
SHELL=/bin/bash
OUTDIR=TMP
BUILD=GRCh38
all: $(OUTDIR)/database.rdf query.01.sparql
/path/to/pache-jena-4.8.0/bin/arq --data=$< --query=query.01.sparql
$(OUTDIR)/database.rdf: $(OUTDIR)/go.rdf $(OUTDIR)/gtf.rdf
mkdir -p $(dir $@)
@lindenb
lindenb / out.log
Created March 25, 2024 08:24
diff bind
(...)
> #### Occupancy Analysis ####
> png("Clustering_Occupancy.png", width= 840, height = 840)
> plot(DBsample, cexRow = 1.4, cexCol = 1.4)
> dev.off()
null device
1
>
> write("DBA COUNT", stderr())
DBA COUNT
@lindenb
lindenb / README.md
Last active March 23, 2024 20:33
Delete Tweets

I want to delete all my tweets without deleting my account.

This script deletes your tweets and repost from twitter without using the Twitter API, just by using the firefox javascript scratchpad.

Chage YOURNAME in the script below.

The script is quite slow but it works so far , I set some long timeout to let the DOM document to (re)load.

May be it could be much faster but I'm not a javascript guy.

@lindenb
lindenb / README.md
Last active February 19, 2024 12:18
compile R as library

MOTIVATION

I'm trying to compile #RStat as a static library with the -fPIC flag (so I can use it within #java #jni)

DOWNLOAD AND COMPILE

rm -rvf  "TMP/R-4.3.2" TMP/jeter.tar.gz
mkdir -p TMP/R-4.3.2/lib/
wget -O TMP/jeter.tar.gz "https://pbil.univ-lyon1.fr/CRAN/src/base/R-4/R-4.3.2.tar.gz"
cd TMP && tar xfz jeter.tar.gz && rm jeter.tar.gz &&  cd R-4.3.2 && \
@lindenb
lindenb / nextflow.log
Created October 19, 2023 17:11
nextflow cut&run. Nothing happens and .nextflow.log contains java stackTrace about aws.
Oct-19 19:04:09.799 [S3TransferManager-6] WARN c.a.i.InstanceMetadataServiceResourceFetcher - Fail to retrieve token
com.amazonaws.SdkClientException: Failed to connect to service endpoint:
at com.amazonaws.internal.EC2ResourceFetcher.doReadResource(EC2ResourceFetcher.java:100)
at com.amazonaws.internal.InstanceMetadataServiceResourceFetcher.getToken(InstanceMetadataServiceResourceFetcher.java:91)
at com.amazonaws.internal.InstanceMetadataServiceResourceFetcher.readResource(InstanceMetadataServiceResourceFetcher.java:69)
at com.amazonaws.internal.EC2ResourceFetcher.readResource(EC2ResourceFetcher.java:66)
at com.amazonaws.auth.InstanceMetadataServiceCredentialsFetcher.getCredentialsEndpoint(InstanceMetadataServiceCredentialsFetcher.java:60)
at com.amazonaws.auth.InstanceMetadataServiceCredentialsFetcher.getCredentialsResponse(InstanceMetadataServiceCredentialsFetcher.java:48)
at com.amazonaws.auth.BaseCredentialsFetcher.fetchCredentials(BaseCredentialsFetcher.java:124)
at com.amazonaws.auth.BaseCre
@lindenb
lindenb / main.nf
Created September 11, 2023 07:01
https://www.biostars.org/p/9574590/ Nextflow - How to pass the yml yaml format input file from an argument to channel as a list
params.samples="NO_FILE"
workflow {
ch = Channel.fromPath(params.samples).
flatMap(F->{
def yaml = new org.yaml.snakeyaml.Yaml();
def map = yaml.load(F);
return map.samples;
});
doIt(ch)