From 3a816db1f4aa113764fa04eef2ffe39c29408cf1 Mon Sep 17 00:00:00 2001 From: Koustav Pal Date: Fri, 12 Jan 2024 11:04:01 +0000 Subject: [PATCH 1/6] Update Dockerfile --- Dockerfile | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 88e7ba1..e5fd57a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,9 @@ RUN apt-get update && apt-get install -y \ liblzma-dev \ libncurses-dev \ zlib1g-dev \ - wget + wget \ + python3 \ + pip && pip install numpy==1.26.3 pandas==1.5.3 mpmath==1.3.0 scipy==1.11.4 statsmodels==0.14.1 tqdm==4.66.1 arch==6.3.0 WORKDIR /tmp/htslib/ RUN git clone https://github.com/samtools/htslib @@ -31,9 +33,9 @@ RUN rm sratoolkit.2.9.6-ubuntu64.tar.gz USER superSTR_user ENV HOME /home/superSTR_user/ WORKDIR /home/superSTR_user/ -RUN git clone https://github.com/bahlolab/superSTR +RUN git clone https://github.com/koustav-pal/superSTR WORKDIR /home/superSTR_user/superSTR/C/ -ENV PATH="/usr/local/sratoolkit/bin:/home/superSTR_user/superSTR/C:${PATH}" +ENV PATH="/usr/local/sratoolkit/bin:/home/superSTR_user/superSTR/C:/home/superSTR_user/superSTR/Python:${PATH}" RUN cmake . RUN make RUN mkdir /home/superSTR_user/.ncbi/ From 1eec4d060b9fa8c3892c05ae0602e50701ca9d90 Mon Sep 17 00:00:00 2001 From: Koustav Pal Date: Fri, 12 Jan 2024 11:04:53 +0000 Subject: [PATCH 2/6] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e5fd57a..9579ba3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -33,7 +33,7 @@ RUN rm sratoolkit.2.9.6-ubuntu64.tar.gz USER superSTR_user ENV HOME /home/superSTR_user/ WORKDIR /home/superSTR_user/ -RUN git clone https://github.com/koustav-pal/superSTR +RUN git clone https://github.com/bahlolab/superSTR WORKDIR /home/superSTR_user/superSTR/C/ ENV PATH="/usr/local/sratoolkit/bin:/home/superSTR_user/superSTR/C:/home/superSTR_user/superSTR/Python:${PATH}" RUN cmake . From 5d753fb2e373530f97ab92abd8c548928fab7850 Mon Sep 17 00:00:00 2001 From: Koustav Pal Date: Fri, 12 Jan 2024 11:20:33 +0000 Subject: [PATCH 3/6] Update screen.py --- Python/screen.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Python/screen.py b/Python/screen.py index ac784cd..bec5a74 100644 --- a/Python/screen.py +++ b/Python/screen.py @@ -40,7 +40,7 @@ def infill(if_df, manifest_df): for add_samp in to_add: add_dict["sample"] = add_samp add_dict["grp"] = manifest_df.loc[add_samp].grp - if_df = if_df.append(add_dict, ignore_index=True) + if_df = if_df.concat(add_dict, ignore_index=True) return if_df From 6cee52f38fd9f3646a4eefda8158462267a82a5a Mon Sep 17 00:00:00 2001 From: Koustav Pal Date: Fri, 12 Jan 2024 11:24:57 +0000 Subject: [PATCH 4/6] Update screen.py --- Python/screen.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Python/screen.py b/Python/screen.py index bec5a74..3bed916 100644 --- a/Python/screen.py +++ b/Python/screen.py @@ -40,7 +40,7 @@ def infill(if_df, manifest_df): for add_samp in to_add: add_dict["sample"] = add_samp add_dict["grp"] = manifest_df.loc[add_samp].grp - if_df = if_df.concat(add_dict, ignore_index=True) + if_df = pd.concat(add_dict, ignore_index=True) return if_df From b764a76b6310b1c7dc75baaa822155133d624cc7 Mon Sep 17 00:00:00 2001 From: Koustav Pal Date: Fri, 12 Jan 2024 11:27:25 +0000 Subject: [PATCH 5/6] Update screen.py From 5228708c99d2b75519f863db373982512d41e55a Mon Sep 17 00:00:00 2001 From: Koustav Pal Date: Fri, 12 Jan 2024 11:52:23 +0000 Subject: [PATCH 6/6] Update screen.py --- Python/screen.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Python/screen.py b/Python/screen.py index 3bed916..ac784cd 100644 --- a/Python/screen.py +++ b/Python/screen.py @@ -40,7 +40,7 @@ def infill(if_df, manifest_df): for add_samp in to_add: add_dict["sample"] = add_samp add_dict["grp"] = manifest_df.loc[add_samp].grp - if_df = pd.concat(add_dict, ignore_index=True) + if_df = if_df.append(add_dict, ignore_index=True) return if_df