apraga/org - Change KVTDFHZ3QKPWGPMHX6SVJQ7DJD76XR3MKOYKOPNVMQOTER3TYRCQC

Today notes

Created by Alexis Praga on May 19, 2024

KVTDFHZ3QKPWGPMHX6SVJQ7DJD76XR3MKOYKOPNVMQOTER3TYRCQC

Dependencies

In channels

main

Change contents

Replacement in projects.org at line 7 [3.179]

B:BD[3.264] → [2.3:69]

**** STRT Dépendences Sarek [0/6]
***** WAIT Package nix Dragmap

[3.264]

[4.139]

**** STRT Dépendences Sarek [0/5]
***** WAIT Package nix Dragmp

Replacement in projects.org at line 11 [3.179]

B:BD[2.105] → [2.105:135]

∅:D[2.135] → [5.169:197]

B:BD[5.169] → [5.169:197]

B:BD[5.197] → [4.186:246]

***** STRT Package nix Tiddlt
SCHEDULED: <2024-05-18 Sat>
- tiddit package ok
- Manque fermi2 : ajouteer dans wrapper

[2.105]

[3.293]

***** WAIT [[file:~/code/nixpkgs/pkgs/by-name/ti/tiddit/package.nix::{][Package nix Tiddit]] : [[https://github.com/NixOS/nixpkgs/pull/312995][PR]]

Replacement in projects.org at line 17 [3.179]
B:BD[3.464] → [2.198:225]
∅:D[2.225] → [4.275:285]
B:BD[4.275] → [4.275:285]
B:BD[4.285] → [2.226:257]
∅:D[2.257] → [4.317:328]
B:BD[4.317] → [4.317:328]
```
***** WAIT Package nix vep
PR soumis
***** WAIT Package nix multiqc
PR soumis
```
[3.464]
[2.258]
```
***** WAIT Package nix vep : PR
***** WAIT Package nix multiqc : PR
```
Replacement in projects.org at line 20 [3.179]
B:BD[2.314] → [2.314:327]
```
***** genome
```
[2.314]
[2.327]
```
***** genome hg38 + hg19
```

Insertion in projects.org at line 23 [3.179]

[2.353]

*** TODO Soumission JCADD 2024
SCHEDULED: <2024-05-27 Mon>
/Entered on/ [2024-05-19 Sun 13:24]

Insertion in projects.org at line 50 [3.179]

[3.831]

** DONE Payer leçon aya <2024-05-19 Sun>
/Entered on/ [2024-05-19 Sun 23:02]

Insertion in projects.org at line 68 [3.179]

[3.1119]

** DONE Contacter DAM pour changement d'adresse
SCHEDULED: <2024-05-19 Sun>
/Entered on/ [2024-05-19 Sun 13:56]
** TODO Convertir notes bactério org-mode
/Entered on/ [2024-05-19 Sun 13:29]
** TODO Converter notes biochimie org-mode
/Entered on/ [2024-05-19 Sun 13:29]
* Maison
:PROPERTIES:
:CATEGORY: maison
:END:
** TODO Contacter RED pour changer adresse sur facture
SCHEDULED: <2024-05-22 Wed>
/Entered on/ [2024-05-19 Sun 13:56]
* Divers
:PROPERTIES:
:CATEGORY: divers
:END:
** TODO Remboursement Allianz Montbéliard -> Grenoble 2024/0523168
/Créé le/ [2024-05-16 Thu 22:44]
2024-03-01
** TODO Justificatif de domicile Caisse Épargne Metz
SCHEDULED: <2024-05-20 Mon>
/Créé le/ [2024-05-17 Fri 21:32]
** TODO Recoudre pantalon rouge
SCHEDULED: <2024-05-20 Mon>
/Entered on/ [2024-05-19 Sun 13:23]
** TODO Changer adresse banque pour Allondaz
SCHEDULED: <2024-05-20 Mon>
/Entered on/ [2024-05-19 Sun 13:24]
* Nix

Replacement in notes/nixpkgs.org at line 42 [6.163095]

B:BD[6.164409] → [6.164409:164431]

B:BD[6.164431] → [3.2245:2314]

* Débugger un paquet
[[id:56f7a57a-1807-4d72-abb2-6420eab119c5][Débugger un paquet nix]]

[6.164409]

[6.164550]

* [[id:56f7a57a-1807-4d72-abb2-6420eab119c5][Débugger un paquet nix]]

File addition: fichiers_bam.org (----------)

[7.188]

:PROPERTIES:
:ID:       baeadc69-3352-4f3f-8d87-0b74ad9c920f
:END:
#+title: Fichiers BAM
#+filetags: bioinfo
* Astuces
** Couper un BAM par chromosome
#+begin_src sh
 bamtools split -in 2200519525-63060439-GRCh38.recal.bam -reference
#+end_src
*Attention* Ne pas utiliser =samtools view= peut causer des soucis car les @SQ vont contenire des références aux autres chromosomes
** Convertir un SAM en BAM
#+begin_src sh
samtools view test.sam -o test.bam
#+end_src

Deletion in notes/debugger_un_paquet_nix.org at line 8 [6.862858]
∅:D[3.2883] → [6.862894:862945]
B:BD[6.862894] → [6.862894:862945]
```
:PROPERTIES:
:CUSTOM_ID: démarrer-un-shell.
:END:
```
Deletion in notes/debugger_un_paquet_nix.org at line 9 [6.862858]
B:BD[6.862957] → [6.862957:862996]
```
:PROPERTIES:
:CUSTOM_ID: nixpkgs
:END:
```
Deletion in notes/debugger_un_paquet_nix.org at line 17 [6.862858]
B:BD[6.863089] → [6.863089:863133]
```
:PROPERTIES:
:CUSTOM_ID: paquet-local
:END:
```
Deletion in notes/debugger_un_paquet_nix.org at line 30 [6.862858]
∅:D[3.2896] → [6.863319:863357]
B:BD[6.863319] → [6.863319:863357]
```
:PROPERTIES:
:CUSTOM_ID: débug
:END:
```
Deletion in notes/debugger_un_paquet_nix.org at line 62 [6.862858]
∅:D[3.2910] → [6.864080:864122]
B:BD[6.864080] → [6.864080:864122]
```
:PROPERTIES:
:CUSTOM_ID: ressources
:END:
```
Replacement in notes/article_joss_bisonex.org at line 25 [4.689]
B:BD[4.1378] → [4.1378:1391]
```
Dépendences
```
[4.1378]
[4.1391]
```
* Dépendences avec Nix
```

Insertion in notes/article_joss_bisonex.org at line 45 [4.689]

[4.1962]


* Assets avec scidataflow
Problèmes :
- pull sur seulement un sous-dossier (à implémenter)
- préparer les données : script bash ?
  - extraire fna.gz -> fna
   #+begin_src sh
find . -name *.fna.gz -exec gunzip {} \;
find . -name *.bwa_index.tar.gz -exec tar xvzf {} \;
   #+end_src

Insertion in journal/20240519 at line 4 [2.1543]

[2.1679]

** 23:43 Package tiddit
Il manquant propagatedBuildInputs pour avoir fermi2 et ropebwt2 à l'exécution
*** Test
  #+begin_src sh
cd ~/code/bisonex/tests
tiddit --sv --bam chr22.bam --ref ~/code/human_genome_assets/sequence/GRCH38/GCA_000001405.15_GRCh38_full_analysis_set.fna
  #+end_src
  où le bam est extrait depuis un run avec `bamtools split`
  ATtention à la concordance sur le nom des chromosomes...

Replacement in inbox.org at line 2 [3.3292]

B:BD[3.3311] → [3.3311:3540]

B:BD[3.3567] → [3.3567:3575]

B:BD[3.3575] → [2.1720:2172]

* TODO Remboursement Allianz Montbéliard -> Grenoble 2024/0523168
/Créé le/ [2024-05-16 Thu 22:44]
2024-03-01
* TODO Justificatif de domicile Caisse Épargne Metz
SCHEDULED: <2024-05-20 Mon>
/Créé le/ [2024-05-17 Fri 21:32]
* Inbox
* TODO Recoudre pantalon rouge
SCHEDULED: <2024-05-20 Mon>
/Entered on/ [2024-05-19 Sun 13:23]
* TODO Changer adresse banque pour Allondaz
SCHEDULED: <2024-05-20 Mon>
/Entered on/ [2024-05-19 Sun 13:24]
* TODO Soumission JCADD 2024
SCHEDULED: <2024-05-27 Mon>
/Entered on/ [2024-05-19 Sun 13:24]
* TODO Convertir notes bactério org-mode
/Entered on/ [2024-05-19 Sun 13:29]
* TODO Converter notes biochimie org-mode
/Entered on/ [2024-05-19 Sun 13:29]

[3.3311]

* TODO Review PR  gitftless 154351
/Entered on/ [2024-05-20 Mon 00:08]

Today notes

Dependencies

In channels

Change contents

Replacement in projects.org at line 7 [3.179]

Replacement in projects.org at line 11 [3.179]

Replacement in projects.org at line 17 [3.179]

Replacement in projects.org at line 20 [3.179]

Insertion in projects.org at line 23 [3.179]

Insertion in projects.org at line 50 [3.179]

Insertion in projects.org at line 68 [3.179]

Replacement in notes/nixpkgs.org at line 42 [6.163095]

File addition: fichiers_bam.org (----------)

Deletion in notes/debugger_un_paquet_nix.org at line 8 [6.862858]

Deletion in notes/debugger_un_paquet_nix.org at line 9 [6.862858]

Deletion in notes/debugger_un_paquet_nix.org at line 17 [6.862858]

Deletion in notes/debugger_un_paquet_nix.org at line 30 [6.862858]

Deletion in notes/debugger_un_paquet_nix.org at line 62 [6.862858]

Replacement in notes/article_joss_bisonex.org at line 25 [4.689]

Insertion in notes/article_joss_bisonex.org at line 45 [4.689]

Insertion in journal/20240519 at line 4 [2.1543]

Replacement in inbox.org at line 2 [3.3292]