apraga/org - Change UPNBONLATA6EOXDE4CPO2ZHJI2XC62YATCJVEMAJ3BSFNLNHY5CQC

Bisonex, workout

Created by Alexis Praga on February 18, 2023

UPNBONLATA6EOXDE4CPO2ZHJI2XC62YATCJVEMAJ3BSFNLNHY5CQC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 5841 [5.1]

[4.647]


* <2023-02-18 Sat> Workout
** Muscle-up
Progrès !
- 4x1 + 4 neg
- 2-1-1-1 + 4 neg
- 2-1-1-1 + 4 neg
** Norwegian curl
- 4
- 4
- 4
** Compression
- 1x9
- 1x9
- 1x9
** Push-up
- 5-3-2
- 5-3-2
- 5-3-2
** Pull-up
- 3-2
- 3-2
- 3-2
** Extension
- 22
- 22
- 22

File addition: bisonex.org_archive (----------)

[6.13]

#    -*- mode: org -*-
Archived entries from file /home/alex/org/projects/bisonex.org
* DONE Vérifier qualité données sur mesocentre
CLOSED: [2023-01-12 Thu 15:48]
:PROPERTIES:
:ARCHIVE_TIME: 2023-01-12 Thu 15:48
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Données
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
** DONE BAM
CLOSED: [2023-01-12 Thu 15:47]
picard ValidateSamFile
On regarde juste le code d'erreur (0 = pas d'erreur)
** DONE Fastq
CLOSED: [2023-01-12 Thu 15:48]
fastqc
Il faut ensuite extraire les zip and chercher les erreur dedans
* KILL Implémenter d’autres pipeline
CLOSED: [2023-01-15 Sun 12:03]
:PROPERTIES:
:ARCHIVE_TIME: 2023-01-15 Sun 12:03
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: KILL
:END:
Voir https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04407-x
** KILL GATK
CLOSED: [2022   -11-11 Fri 20:01]
https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README
A priori, respecte les bonnes pratiques
** KILL Essayer snmake avec bonne pratiques
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/main/.github/workflows/main.yml
Installer Mamba (micromamba ne fonctionne pas sous nix)
Ne fonctionne pas sous WSL2... MultiQC n’est pas assez à jour
Problèmes de versions...
** KILL Sarek
CLOSED: [2022-12-11 Sun 11:09]
*** Dépendences
**** Nix
#+begin_src sh
 nix profile install nixpkgs#mosdepth nixpkgs#python3
  nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
***** KILL derivation nix pour profile complet
CLOSED: [2022-12-11 Sun 11:09]
**** KILL Sans nix
CLOSED: [2022-09-24 Sat 10:20]
On utilise conda
#+begin_src sh
module unload nix
module load anaconda3@2021.05/gcc-12.1.0
module load nextflow@22.04.0/gcc-12.1.0
module load openjdk@11.0.14.1_1/gcc-12.1.0
nextflow run nf-core/sarek -profile conda,test --executor slurm --queue smp --outdir test -resume
#+end_src
Essai 1: erreurs de permissions, corrigé en relancant le programme
#+begin_quote
  Failed to create Conda environment
  command: conda create --mkdir --yes --quiet --prefix /Work/Users/apraga/test-sarek/work/conda/env-2d53b1db50de676670cf1a91ef0cf6db bioconda::tabix=1.11
  status : 1
  message:
    NotWritableError: The current user does not have write permissions to a required path.
      path: /Home/Users/apraga/.conda/pkgs/urls.txt
      uid: 1696
      gid: 513
    If you feel that permissions on this path are set incorrectly, you can manually
    change them by executing
      $ sudo chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
#+end_quote
Corrigé avec
#+begin_src sh
      chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
#+end_src
Mais problème de proxy
*** KILL Dérivation nix pour modules python
CLOSED: [2022-12-11 Sun 11:09]
*** KILL Lancer sarek en mode test
CLOSED: [2022-12-11 Sun 11:09]
#+begin_src sh
  nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
*** KILL Lancer sarek sur données allégées
CLOSED: [2022-12-11 Sun 11:09]
* DONE Essai 1
CLOSED: [2023-02-13 Mon 11:50]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-14 Tue 10:42
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Nouveau workflow/Dépendences avec Nix/hap.py/Faire fonctionner Tests
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
Problème avec chemin python pour pysam : Tools/__init__.py échoue mais on peut utilise build/bin/hap.py
#+begin_src
nix develop .#hap-py
$ genericBuild
#+end_src
On lance donc les tests à la main (trop d'erreurs sur les chemins)
#+begin_src
# OK !
HCDIR=build/bin build/bin/test_haplotypes
# OK !
bash src/sh/make_hg19.sh
HCDIR=build/bin HG19=hg19.fa bash src/sh/run_multimer
ge_test.sh
#+end_src
Écheck sur
$ HCDIR=build/bin bash src/sh/run_hapenum_test.sh
Traceback (most recent call last):
  File "build/bin/hap.py", line 26, in <module>
    import pysam
  File "/nix/store/3w2v5cl4x6ddq4281awcab9412r5gkaw-python3-3.10.9-env/lib/python3.10/site-packages/pysam/__init__.py", line 4, in <module>
    from pysam.libchtslib import *
ImportError: No module named libchtslib
IL faut commenter detect var

Replacement in projects/bisonex.org at line 850 [6.35]

B:BD[7.344] → [7.344:404]

**** TODO Sérialiser json pour écrire données de sorties

[8.718]

[7.404]

**** DONE Sérialiser json pour écrire données de sorties
CLOSED: [2023-02-17 Fri 19:25]

Deletion in projects/bisonex.org at line 865 [6.35]
B:BD[9.904] → [2.15:15]
∅:D[2.15] → [7.2133:2169]
∅:D[10.729] → [7.2133:2169]
∅:D[9.904] → [7.2133:2169]
B:BD[7.2133] → [7.2133:2169]
```
**** TODO Version avec rtg-tools |
```
Insertion in projects/bisonex.org at line 866 [6.35]
[3.98]
[3.98]
```
**** TODO Version avec rtg-tools
```

Replacement in projects/bisonex.org at line 901 [6.35]

B:BD[11.473] → [11.473:2412]

B:BD[11.2412] → [3.942:1035]

∅:D[3.1035] → [11.2477:2949]

B:BD[11.2477] → [11.2477:2949]

****** vcfeval : echec
#+begin_src sh
cd /Work/Groups/bisonex/data/NA12878/precisionChallenge
curl -O https://data.nist.gov/od/ds/ark:/88434/mds2-2336/submission_vcfs/0GOOR/0GOOR_HG002.vcf.gz
bcftools annotate --rename-chrs  /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping.txt 0GOOR_HG002.vcf.gz -o 0GOOR_HG002_renamed.vcf.gz
tabix  0GOOR_HG002_renamed.vcf.gz
#+end_src
Soumission
#+begin_src slurm
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G
module load nix/2.11.0
export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna
dir=/Work/Groups/bisonex/data/NA12878/
rtg vcfeval -b  $dir/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz  \
        --bed-regions ${dir}/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed \
        -c ${dir}/precisionChallenge/0GOOR_HG002_renamed.vcf.gz \
        -o test-0GOOR -t /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.sdf
#rtg vcfeval -b  $dir/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz  --bed-regions ${dir}/benchmark-exons.bed -c files/vcf/NA12878_NIST7035_vep_annot.vcf.gz  -o test-rtg -t /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.sdf
#+end_src
Résultat :
VCF header does not contain a FORMAT field named GQ
There were 112 problematic called variants skipped during loading (see vcfeval.log for details).
There were 2303523 variants not thresholded in ROC data files due to missing or invalid GQ (FORMAT) values.
Could not select maximized F-measure threshold from ROC data, only un-thresholded statistics will be shown. Consider selecting a different scoring attribute with --vcf-score-field
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
     None             938101         934445    1369078    1276425     0.4057       0.4236     0.4144
****** DONE sans vcfeval (utilisé pour le challenge) : echec
CLOSED: [2023-02-09 Thu 21:55]
#+begin_src slurm
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G
module load nix/2.11.0
export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna
dir=/Work/Groups/bisonex/data/NA12878/
hap.py $dir/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz  \
        ${dir}/precisionChallenge/0GOOR_HG002_renamed.vcf.gz \
        -f ${dir}/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed \
        -o test
#+end_src

[11.473]

[11.2949]

Le problème venait 1. de l'ADN et 2. du renommage des chromosomes qui était faux
****** DONE HG002
CLOSED: [2023-02-17 Fri 19:31]

Replacement in projects/bisonex.org at line 905 [6.35]

B:BD[11.3109] → [11.3109:4199]

B:BD[11.4199] → [3.1036:1130]

∅:D[10.781] → [11.4225:4470]

∅:D[3.1130] → [11.4225:4470]

B:BD[11.4225] → [11.4225:4470]

B:BD[11.4470] → [10.782:794]

∅:D[10.794] → [12.133:318]

B:BD[11.4511] → [12.133:318]

B:BD[12.318] → [10.795:805]

∅:D[10.805] → [12.318:319]

B:BD[12.318] → [12.318:319]

B:BD[12.319] → [3.1131:1176]

∅:D[3.1176] → [10.857:1051]

B:BD[10.857] → [10.857:1051]

B:BD[10.1051] → [3.1177:1278]

INDEL    ALL       276768    102437    174331      1156702    211537     842303  53768  58006       0.370119          0.327170        0.728194         0.347322
INDEL   PASS       276768    102437    174331      1156702    211537     842303  53768  58006       0.370119          0.327170        0.728194         0.347322
  SNP    ALL      1937706    835470   1102236      5666020   1160590    3669981 437793  21058       0.431164          0.418553        0.647718         0.424765
  SNP   PASS      1937706    835470   1102236      5666020   1160590    3669981 437793  21058       0.431164          0.418553        0.647718         0.424765
  On est censé avoir : https://data.nist.gov/od/ds/ark:/88434/mds2-2336/benchmarking_results/0GOOR/0GOOR_HG002.extended.csv
 Type  Filter  METRIC.Recall    METRIC.Precision    METRIC.Frac_NA    METRIC.F1_Score
INDEL  ALL     0.935776    0.903997    0.523369    0.919612
INDEL  PASS    0.935776    0.903997    0.523369    0.919612
SNP    ALL     0.998554    0.99395    0.403126    0.996247
SNP    PASS    0.998554    0.99395    0.403126    0.996247
****** DONE Avec chr originels + génome de référence : idem
CLOSED: [2023-02-09 Thu 21:55]
#+begin_src
awk '{
        if($0 !~ /^#/)
            print "chr"$0;
        else if(match($0,/(##contig=<ID=)(.*)/,m))
            print m[1]"chr"m[2];
        else print $0
      }' 0GOOR_HG002.vcf | gzip -c > 0GOOR_HG002_chr.vcf.gz
#+end_src
#+begin_src
curl -O https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz /Work/Groups/bisonex/data/genome/GRCh38/
#+end_src
segmentation fault... Il faut unzip le fasta
#+begin_src
cd  /Work/Groups/bisonex/data/genome/GRCh38/
 gunzip GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz
 samtools faidx GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
#+end_src
#+begin_src slurm
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G

[11.3109]

[3.1278]

INDEL    ALL       525466    491355     34111      1156702     57724     605307   9384  25027       0.935084          0.895313        0.523304         0.914766
INDEL   PASS       525466    491355     34111      1156702     57724     605307   9384  25027       0.935084          0.895313        0.523304         0.914766
  SNP    ALL      3365115   3358399      6716      5666020     21995    2284364   4194   1125       0.998004          0.993496        0.403169         0.995745
  SNP   PASS      3365115   3358399      6716      5666020     21995    2284364   4194   1125       0.998004          0.993496        0.403169         0.995745

Replacement in projects/bisonex.org at line 910 [6.35]

B:BD[3.1279] → [3.1279:2379]

∅:D[10.1051] → [12.341:365]

∅:D[3.2379] → [12.341:365]

B:BD[12.341] → [12.341:365]

B:BD[12.467] → [12.467:488]

module load nix/2.11.0
dir=/Work/Groups/bisonex/data/NA12878/
truth=${dir}/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
#ref=script/files/vcf/NA12878_NIST7035.vcf
ref=${dir}/precisionChallenge/0GOOR_HG002_chr.vcf.gz
bed=${dir}/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed
fasta=/Work/Groups/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
hap.py $truth $ref -f $bed -r $fasta -o test
#+end_src
Même résultats
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL       467684    174199    293485      1156702    358998     622785  90229  99609       0.372472          0.327615
INDEL   PASS       467684    174199    293485      1156702    358998     622785  90229  99609       0.372472          0.327615
  SNP    ALL      3254352   1410388   1843964      5666020   1953278    2302401 735823  36239       0.433385          0.419293
  SNP   PASS      3254352   1410388   1843964      5666020   1953278    2302401 735823  36239       0.433385          0.419293
****** Vérifier FN
***** TODO Avec python2
****** TODO avec nix

[3.1279]

[12.488]

 TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
                    NaN                     NaN                   1.528276                   2.752637
                    NaN                     NaN                   1.528276                   2.752637
               2.100129                1.473519                   1.581196                   1.795603
               2.100129                1.473519                   1.581196                   1.795603
***** KILL Avec python2
CLOSED: [2023-02-17 Fri 19:25]
****** KILL avec nix
CLOSED: [2023-02-17 Fri 19:25]

Replacement in projects/bisonex.org at line 920 [6.35]
B:BD[12.532] → [3.2380:2403]
```
****** TODO avec conda
```
[12.532]
[3.2403]
```
****** KILL avec conda
CLOSED: [2023-02-17 Fri 19:25]
```
Replacement in projects/bisonex.org at line 944 [6.35]
B:BD[3.3493] → [3.3493:3512]
```
****** avec docker
```
[3.3493]
[3.3512]
```
****** KILL avec docker
CLOSED: [2023-02-17 Fri 19:25]
```

Insertion in projects/bisonex.org at line 2806 [6.35]

[13.28]

[8.752]

**** Nextflow
***** DONE Télécharger NA12878 (HG001)
CLOSED: [2023-02-17 Fri 19:29]
***** DONE Télécharger Ashkenazy trio HG002
CLOSED: [2023-02-17 Fri 19:29]
***** DONE Renommer les chromosomes
CLOSED: [2023-02-17 Fri 19:30]
***** TODO Genome de reference NCBI
Téléchargé mais index non stocké dars /Work TODO
**** Notes

Replacement in projects/bisonex.org at line 2817 [6.35]
∅:D[13.117] → [7.3250:3251]
B:BD[7.3250] → [7.3250:3251]
[8.799]
[7.3524]
```
**** Comparaison
```

Replacement in projects/bisonex.org at line 2835 [6.35]

B:BD[14.446] → [11.4573:4615]

∅:D[15.168] → [13.187:250]

∅:D[16.350] → [13.187:250]

∅:D[11.4615] → [13.187:250]

B:BD[13.187] → [13.187:250]

**** TODO beaucoup trop de faux négatifs
***** DONE Test 1 : vep annot : beaucoup trop de faux négatif

[14.446]

[14.487]

***** KILL beaucoup trop de faux négatifs
CLOSED: [2023-02-17 Fri 19:37]
****** DONE Test 1 : vep annot : beaucoup trop de faux négatif

Replacement in projects/bisonex.org at line 2844 [6.35]
B:BD[14.1567] → [13.251:296]
```
***** KILL Test 3 : indexer vcf de reference
```
[14.1567]
[13.296]
```
****** KILL Test 3 : indexer vcf de reference
```
Replacement in projects/bisonex.org at line 2847 [6.35]
B:BD[13.394] → [13.394:435]
```
***** DONE Test 3 sans filtre vep : idem
```
[13.394]
[13.435]
```
****** DONE Test 3 sans filtre vep : idem
```

Replacement in projects/bisonex.org at line 2855 [6.35]

B:BD[17.1743] → [13.468:520]

***** DONE Test 4 avec vcfeval sur vep_annot : idem

[17.1743]

[13.520]

****** DONE Test 4 avec vcfeval sur vep_annot : idem

Replacement in projects/bisonex.org at line 2878 [6.35]
B:BD[17.2991] → [16.351:400]
```
***** DONE Regarder quelques variants à la main
```
[17.2991]
[16.400]
```
****** DONE Regarder quelques variants à la main
```

Insertion in projects/bisonex.org at line 2905 [6.35]

[16.1610]

[15.890]

******* TODO Tests après correction bug dans noms de chromosome : precision ~ ok, recall très mauvais -> trop de FN ?
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL         7230       321      6909         1500       290        888     27     18       0.044398          0.526144
INDEL   PASS         7230       321      6909         1500       290        888     27     18       0.044398          0.526144
  SNP    ALL        59052      1653     57399         3338       101       1583     12      2       0.027992          0.942450
  SNP   PASS        59052      1653     57399         3338       101       1583     12      2       0.027992          0.942450

Insertion in projects/bisonex.org at line 2912 [6.35]

[15.891]

[11.4738]

 METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
       0.592000         0.081887                     NaN                     NaN                    1.54733                   6.129187
       0.592000         0.081887                     NaN                     NaN                    1.54733                   6.129187
       0.474236         0.054370                2.433271                1.861183                    1.57523                   2.703663
       0.474236         0.054370                2.433271                1.861183                    1.57523                   2.703663
******* Vérifier exons
On a l'union des exons de tous les transcripts...
Il faudrait un .bed d'illumina
On teste Twist for Illumina Exome 2.0 Plus BED File (hg19) sur https://support.illumina.com/downloads/nextera-flex-for-enrichment-BED-files.html
Conversion en hg38 avec ucsc
Renommage des chromosomes
#+begin_src
sed 's:^:s/chr:;s:chrMT:chrM:;s:\s:\\t/:;s:$:\\t/:' ../../genome/GRCh38.p13/chromosome_mapping.txt > pattern.sed
sed -i.bak -f pattern.sed illumina_exons.bed
bedtools intersect -a HG001_GRCh38_1_22_v4.2.1_benchmark.bed -b illumina_exons.bed > HG001_GRCh38_1_22_v4.2.1_benchmark_illumina_exons.bed
#+end_src
Intersection
******* Erreur dans le paramère : -f au lieu de -R !!
Il faut supprimer les overlap (et trier avant)
 bedtools sort -i illumina_exons.bed > illumina_exons.bed.sorted
 bedtools merge -i illumina_exons.bed.sorted > HG001_GRCh38_1_22_v4.2.1_benchmark_illumina_exons.be

Deletion in projects/bisonex.org at line 2938 [6.35]

B:BD[16.2032] → [11.4757:6664]

∅:D[11.6664] → [16.2032:2033]

B:BD[16.2032] → [16.2032:2033]

****  Version avec python 2 sans nix
nix profile install nixpkgs#autoconf
nix profile install nixpkgs#cmake
On cherche boost avec ls /nix/store/*boost*
 python2 install.py install-hap.py --boost-root /nix/store/4djr55cmnfahbg6i6wr8p3ga66gs09gi-boost-1.79.0
 Pour utiliser le boost de nix, il faut patcher pour utiliser la version non static
 #+begin_src diff
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 307a3b9..806d064 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,16 +32,16 @@ if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
     message(FATAL_ERROR "Building external dependencies has failed")
 endif()
-set(Boost_USE_STATIC_LIBS        ON)  # only find static libs
+#set(Boost_USE_STATIC_LIBS        ON)  # only find static libs
 set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME     ON)
+#set(Boost_USE_STATIC_RUNTIME     ON)
 # un-break library finding
-set(Boost_NO_BOOST_CMAKE         ON)
-set(Boost_NO_SYSTEM_PATHS        ON)
+#set(Boost_NO_BOOST_CMAKE         ON)
+#set(Boost_NO_SYSTEM_PATHS        ON)
-set(BOOST_ROOT ${CMAKE_BINARY_DIR})
-message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
+#set(BOOST_ROOT ${CMAKE_BINARY_DIR})
+#message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
 find_package(Boost 1.55.0 COMPONENTS thread iostreams regex unit_test_framework filesystem system program_options REQUIRED)
 include_directories(${Boost_INCLUDE_DIRS})
 #+end_src
 Echeck à la compilatio
 On essaye la dernière version de boost:
#+begin_src sh
cd external
wget https://boostorg.jfrog.io/artifactory/main/release/1.81.0/source/boost_1_81_0.tar.bz2
sed -i.bak 's/boost_subset_1_58_0/boost_1_81_0/' external/make_dependencies.sh
#+end_src
On essaye avec boost en static dans nix :
 nix-shell -E "with import <nixpkgs> {}; pkgs.boost.override{ enableStatic = true;}"

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[18.596]
[18.596]
```
*** TODO Benefits of Old Laws
*** TODO Pride of time
```

Bisonex, workout

Dependencies

In channels

Change contents

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