Installing ipython and numpy in the container.

numpy is to try to force numpy support in pyBedTools.

PRO-seq/PRO-seq.snakefile

@@ -1194,7 +1194,7 @@ rule merge_bigwig_reps:
                         warn(f"The bigwig files without {chrom} will be skipped.\n")
                     to_use = [bw for bw in bws if chrom in bw.chroms()]
                     if to_use:
-                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
+                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
                     else:
                         means = np.zeros(chrom_len)
                     # bin size is 10

RNA_Seq_Cecere/RNA-seq.snakefile

@@ -1510,7 +1510,7 @@ rule merge_bigwig_reps:
                         warn(f"The bigwig files without {chrom} will be skipped.\n")
                     to_use = [bw for bw in bws if chrom in bw.chroms()]
                     if to_use:
-                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
+                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
                     else:
                         means = np.zeros(chrom_len)
                     # bin size is 10

Ribo-seq/Ribo-seq.snakefile

@@ -1871,7 +1871,7 @@ rule merge_bigwig_reps:
                         warn(f"The bigwig files without {chrom} will be skipped.\n")
                     to_use = [bw for bw in bws if chrom in bw.chroms()]
                     if to_use:
-                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
+                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
                     else:
                         means = np.zeros(chrom_len)
                     # bin size is 10
@@ -1909,7 +1909,7 @@ rule make_bigwig_ratios:
                 for (chrom, chrom_len) in bw_out.chroms().items():
                     assert cond_bw.chroms()[chrom] == chrom_len
                     #ratios = np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len))
-                    ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len)))
+                    ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len, numpy=True), ref_bw.values(chrom, 0, chrom_len, numpy=True)))
                     # bin size is 10
                     bw_out.addEntries(chrom, 0, values=np.nan_to_num(ratios[0::10]), span=10, step=10)
                 bw_out.close()

singularity/Makefile

@@ -17,6 +17,7 @@ install: run_pipeline run_pipeline.sh workflows_shell.sh
 	done
 	ln -sfn $(PREFIX)_$(VERSION) $(PREFIX)
 
+# TODO: Bind home on temporary directory at build time in order to decrease "pollution" risks?
 # Should depend on the rest of the repository.
 run_pipeline: run_pipeline.def
 	nohup sh -c "yes | sudo singularity build run_pipeline run_pipeline.def > build.err 2>&1" &

singularity/run_pipeline.def

@@ -83,6 +83,10 @@ From:python:3.7-buster
 	# (that will be mounted during singularity build)
 	export PYTHONNOUSERSITE=1
 	python3.7 -m pip install --upgrade pip
+	# Useful for experimenting in shell mode
+	python3.7 -m pip install ipython
+	# Should be installed before pyBedTools for the latter to have numpy support
+	python3.7 -m pip install numpy
 	# Needs to install before custom pybedtools
 	# python3.7 -m pip install pysam
 	# To get scipy properly built as requirement:

small_RNA-seq/small_RNA-seq.snakefile

@@ -2841,7 +2841,7 @@ rule merge_bigwig_reps:
                         raise
                     to_use = [bw for bw in bws if chrom in bw.chroms()]
                     if to_use:
-                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
+                        means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
                     else:
                         means = np.zeros(chrom_len)
                     # bin size is 10
@@ -2882,7 +2882,7 @@ rule make_bigwig_ratios:
                 for (chrom, chrom_len) in bw_out.chroms().items():
                     assert cond_bw.chroms()[chrom] == chrom_len
                     #ratios = np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len))
-                    ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len)))
+                    ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len, numpy=True), ref_bw.values(chrom, 0, chrom_len, numpy=True)))
                     # bin size is 10
                     bw_out.addEntries(chrom, 0, values=np.nan_to_num(ratios[0::10]), span=10, step=10)
                 bw_out.close()