Skip to content

Instantly share code, notes, and snippets.

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

Pierre Lindenbaum lindenb

😶
I hate people.
View GitHub Profile
@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 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 / 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 / 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)
@lindenb
lindenb / bio-anchor.html
Created August 28, 2023 16:20
A first test with WebComponent, extending HTMLElement javascript bioinformatics
<html>
<head>
</head>
<body>
<bio-anchor build="hg38">rs25</bio-anchor> and
<bio-anchor build="hg38">ENSG00000005108</bio-anchor>
<bio-anchor build="hg38">chr1:1234-1235</bio-anchor>
<bio-anchor build="hg38">xxx</bio-anchor>
</body>
@lindenb
lindenb / Makefile
Created August 3, 2023 12:29
biostars9571322 Mafile based ngs worfklow for tutorial
# input is
# DATA/father.R1.fq.gz
# DATA/father.R2.fq.gz
# DATA/mother.R1.fq.gz
# DATA/mother.R2.fq.gz
# DATA/child.R1.fq.gz
# DATA/child.R2.fq.gz
#
define mapreads
@lindenb
lindenb / Artists.md
Created July 3, 2023 11:46
matériel artistes art artist pen pencil paper

Boulet

  • carbon pen platinium DP800S
  • aquarelle winsor & newton
  • pinceaux "Raphaël*
  • papier 250g Clairefontaine
@lindenb
lindenb / chatGPT. monopoly.md
Created April 23, 2023 16:37
Génère moi un jeu de plateau inspiré de #Monopoly se situant dans un labo de Recherche en génétique. L'argent est remplacé par des publications.

Pas de problème, voici les règles pour un jeu de plateau inspiré de Monopoly, mais situé dans un laboratoire de recherche en génétique, où les joueurs achètent des laboratoires plutôt que des propriétés :

Matériel :

  • Plateau de jeu
  • Cartes "Chercheurs invités"
  • Cartes "Subventions"
  • Pions (molécule d'ADN, microscope, fiole, pipette, gant de laboratoire)
  • Billets de publications scientifiques (au lieu d'argent)
  • Laboratoires (au lieu de propriétés)
@lindenb
lindenb / README.md
Last active February 15, 2023 21:21
Biostar Images vs text carbon planet climate

Don't upload images when you can just copy and paste the text.

The following PNG image has a weight of 357,000 bytes

https://www.biostars.org/media/images/8be0316c-0f5a-4e5b-a769-1e4d0afb

while the text containing the very same information is about only 1,109 bytes, hence a much lower carbon footprint.

##sequence-region JAFJXZ010000052.1 1 250