# No FileSystem for scheme "gs" **URL:** \ **Category:** Hail Batch & General Cloud\ **Created:** [June 20, 2024, 8:35am UTC](https://discuss.hail.is/t/no-filesystem-for-scheme-gs/3885 "2024-06-20T08:35:40Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Newbie](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/newbie/32/1163_2.png) [@Newbie](https://discuss.hail.is/u/Newbie)\ **Post date:** [June 20, 2024, 8:35am UTC](https://discuss.hail.is/t/no-filesystem-for-scheme-gs/3885/1 "2024-06-20T08:35:40Z")
Hi all, I know that this topic has been raised already several times but I am still facing the issue in the title. I am interested in reading the files from the gnomAD project. Hail version: ```python pip show hail Name: hail Version: 0.2.130 Summary: Scalable library for exploring and analyzing genomic data. Home-page: https://hail.is Author: Hail Team Author-email: hail@broadinstitute.org License: Location: /home/aih/antonio.nappi/miniconda3/envs/pytorch113/lib/python3.10/site-packages Requires: aiodns, aiohttp, avro, azure-identity, azure-mgmt-storage, azure-storage-blob, bokeh, boto3, botocore, decorator, Deprecated, dill, frozenlist, google-auth, google-auth-oauthlib, humanize, janus, jproperties, nest-asyncio, numpy, orjson, pandas, parsimonious, plotly, pyspark, python-json-logger, pyyaml, requests, rich, scipy, sortedcontainers, tabulate, typer, uvloop ``` command that I am executing: ```python import hail as hl mt = hl.read_matrix_table( 'gs://gcp-public-data--gnomad/release/4.1/ht/exomes/gnomad.exomes.v4.1.sites.ht' ) mt = mt.head(100_000) sites = mt.collect() ``` I get the following error ```python Hail version: 0.2.130-bea04d9c79b5 Error summary: UnsupportedFileSystemException: No FileSystem for scheme "gs" ``` I have installed hail into a singularity container, maybe this is the problem? ---
**Author:** ![danielgoldstein](https://avatars.discourse-cdn.com/v4/letter/d/dbc845/32.png) [@danielgoldstein](https://discuss.hail.is/u/danielgoldstein)\ **Post date:** [June 20, 2024, 4:49pm UTC](https://discuss.hail.is/t/no-filesystem-for-scheme-gs/3885/2 "2024-06-20T16:49:41Z")
Hello @Newbie, have you installed the [GCS Connector](https://github.com/broadinstitute/install-gcs-connector)? That dependency is necessary for Spark (and by extension Hail in your setup) to read from GCS, so you’ll need to install that in your singularity container to get your script working. ---
**Author:** ![Newbie](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/newbie/32/1163_2.png) [@Newbie](https://discuss.hail.is/u/Newbie)\ **Post date:** [June 21, 2024, 9:51am UTC](https://discuss.hail.is/t/no-filesystem-for-scheme-gs/3885/3 "2024-06-21T09:51:02Z")
Hi @danielgoldstein thanks for your answer 🙂 unfortunately I don’t think that the error is there since I should have installed in the singularity container. I post here the config file for the container. ```python Bootstrap: docker 2 From: continuumio/miniconda3 3 4 %environment 5 # Set DEBIAN_FRONTEND to noninteractive to avoid prompts 6 export DEBIAN_FRONTEND=noninteractive 7 # Activate Conda environment 8 source activate gb 9 10 %post 11 export DEBIAN_FRONTEND=noninteractive 12 13 # Install dependencies required by PostgreSQL 14 apt-get update && apt-get install -y --no-install-recommends \ 15 wget ca-certificates \ 16 libreadline-dev zlib1g-dev \ 17 libssl-dev build-essential \ 18 libxml2-dev libxslt1-dev \ 19 libffi-dev liblzma-dev \ 20 locales libpq-dev \ 21 openjdk-11-jdk curl tar vim nano \ 22 g++ \ 23 python3 python3-pip \ 24 libopenblas-dev liblapack-dev \ 25 liblz4-dev \ 26 python3-pip \ 27 git \ 28 build-essential \ 29 maven 30 31 # Install necessary Python packages 32 pip install numpy scipy 33 34 # Set Java 35 echo 'export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64' >> /etc/profile 36 echo 'export PATH=$JAVA_HOME/bin:$PATH' >> /etc/profile 37 # Download and extract Hadoop 38 wget https://downloads.apache.org/hadoop/common/hadoop-3.3.6/hadoop-3.3.6.tar.gz 39 tar -xzvf hadoop-3.3.6.tar.gz -C /opt 40 mv /opt/hadoop-3.3.6 /opt/hadoop 41 # Download the Google Cloud Storage connector 42 wget https://storage.googleapis.com/hadoop-lib/gcs/gcs-connector-hadoop3-latest.jar -P /opt/hadoop/share/hadoop/common 43 44 # Clean up 45 rm hadoop-3.3.6.tar.gz 46 47 # Create Hadoop configuration directory 48 mkdir -p /opt/hadoop/etc/hadoop # Create Hadoop configuration directory 48 mkdir -p /opt/hadoop/etc/hadoop 49 50 # Add GCS connector configuration to core-site.xml 51 echo ' 52 53 fs.gs.impl 54 com.google.cloud.hadoop.fs.gcs.GoogleHadoopFileSystem 55 56 57 fs.AbstractFileSystem.gs.impl 58 com.google.cloud.hadoop.fs.gcs.GoogleHadoopFS 59 60 61 google.cloud.auth.service.account.enable 62 false 63 64 65 google.cloud.auth.application.default 66 true 67 68 ' > /opt/hadoop/etc/hadoop/core-site.xml 69 # Download and extract Spark 3.3.4 70 wget https://archive.apache.org/dist/spark/spark-3.3.4/spark-3.3.4-bin-hadoop3.tgz 71 tar -xzvf spark-3.3.4-bin-hadoop3.tgz -C /opt 72 mv /opt/spark-3.3.4-bin-hadoop3 /opt/spark 73 rm spark-3.3.4-bin-hadoop3.tgz 74 # Install Google Cloud SDK 75 wget https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-367.0.0-linux-x86_64.tar.gz 76 tar -xf google-cloud-sdk-367.0.0-linux-x86_64.tar.gz 77 ./google-cloud-sdk/install.sh -q 78 ./google-cloud-sdk/bin/gcloud components update -q # Clean up 81 rm google-cloud-sdk-367.0.0-linux-x86_64.tar.gz 82 83 # Initialize gcloud (you may need to do this manually after installation or use a service account key) 84 echo 'source /google-cloud-sdk/path.bash.inc' >> ~/.bashrc 85 # Download pre-built Hail JAR 86 git clone https://github.com/hail-is/hail.git 87 cd hail/hail 88 make install-on-cluster HAIL_COMPILE_NATIVES=1 SCALA_VERSION=2.12.18 SPARK_VERSION=3.3.2 89 # Install PostgreSQL and its dependencies 90 apt-get install -y --no-install-recommends \ 91 postgresql postgresql-contrib 92 93 # Ensure all packages are configured properly 94 dpkg --configure -a 95 96 # Remove existing PostgreSQL data directory if it exists 97 if [-d /var/lib/postgresql/13/main]; then 98 rm -rf /var/lib/postgresql/13/main 99 fi 100 101 # Create PostgreSQL data directory and set ownership to postgres 102 mkdir -p /var/lib/postgresql/13/main 103 chown -R postgres:postgres /var/lib/postgresql 104 105 # Initialize PostgreSQL database cluster as postgres user 106 su postgres -c "/usr/lib/postgresql/13/bin/initdb -D /var/lib/postgresql/13/main" 107 108 # Start PostgreSQL service to set password and keep it running 109 su postgres -c "/usr/lib/postgresql/13/bin/pg_ctl -D /var/lib/postgresql/13/main -l /var/log/postgresql/logfile start" 110 su postgres -c "psql -c \"ALTER USER postgres PASSWORD 'password';\"" 111 112 # Setting up Conda environment 113 echo "Setting up Conda environment" 114 conda update -n base -c defaults conda 115 conda env create -f /requirements.yml 116 117 # Clean up Conda cache to free up space 118 conda clean --all --yes 119 rm -rf /opt/conda/pkgs/* 120 121 echo "Conda setup complete." 122 %environment 123 export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64 124 export PATH=$JAVA_HOME/bin:$PATH 125 export PATH=/usr/local/bin:$PATH 126 export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64 127 export HADOOP_HOME=/opt/hadoop 128 export PATH=$HADOOP_HOME/bin:$HADOOP_HOME/sbin:$PATH export CLASSPATH=$HADOOP_HOME/share/hadoop/common/gcs-connector-hadoop3-latest.jar:$CLASSPATH 130 export SPARK_CLASSPATH=$HADOOP_HOME/share/hadoop/common/gcs-connector-hadoop3-latest.jar 131 export SPARK_HOME=/opt/spark 132 export HAIL_HOME=/opt/hail 133 134 %files 135 /lustre/groups/casale/code/users/antonio.nappi/genebass_results/requirements.yml /requirements.yml 136 %runscript 137 # Start PostgreSQL service as postgres user and activate Conda environment 138 su postgres -c "/usr/lib/postgresql/13/bin/pg_ctl -D /var/lib/postgresql/13/main -l /var/log/postgresql/logfile start" 139 source activate gb 140 echo "Starting container with PostgreSQL and Conda environment" 141 exec "$@" ```